TL;DR: How does one design dungeons and encounters, as well as pace a campagin?
Not every adventure has to deal with the end-game. Drop minor hints initially, then more blatant hints, but without yet revealing what the hints are pointing at.
This is sort of long-winded, but one of the best ways I know to demonstrate this is by example.
I'm running a Viking-themed gestalt game that started at first level, and has recently hit 15th level. From 6th to ~12th level I ran a heavily revamped version of Red Hand of Doom that ended in the "Battle of Brindol" at a planar breach with demons pouring through. The 20th level climax involves a great wyrm white dragon, and the cursed silver of Andvari (from Norse Myth), silver that picked up an additional trait from its time hoarded by Fafnir (who held said silver in Norse Myth). The hoard had come to be owned by someone who was then slowly transformed into a dragon by its curse. Some of that cursed silver ended getting out into the economy, and thus dragons, which have not been common, are showing up, because its possessors are being transformed by the curse.
On the first adventure the PC's were on (hunting down a fugitive), they came across a corpse that had a note addressed to some of the wise women in the PCs' homeland. It was from a neighboring ruler (a high-level druid) mentioning that the signs and portents are aligning, so the wise women should make preparations. It was left purposefully vague, both as a means of keeping the information private if any other eyes saw the note, and because this was only the first clue of the 12th level climax of a planar alignment occurring that would allow demons from the underworld to enter Midgard through a gateway.
Around 5th level, at a celebratory feast following the coronation of a young king, a skald recited the tale of Sigurd's slaying of Fafnir, and his taking of the silver, despite the dragon's warning that the silver would lead to his ruin. (All of this is directly from Norse myth.) It ended by mentioning Sigurd's fall (his love affair with Brynhild is the subject of a famous opera) and vaguely referenced the downfall of his house (the Volsungs). [I think there was one smaller clue about this earlier, but I can't recall what it was.]
Back-story that the PC's don't know is that a great conquering army of trolls about 400 years ago extorted wealth from many regions, and got the cursed silver as protection money. The commander was a Half-Fiend Ice Troll, and he took all the cursed silver, and was transformed into a Great Wyrm White Dragon.
Shortly after the coronation where they heard the tale of Sigurd, the conversion of the Red Hand of Doom adventure began. They were traveling cross-country, and were ambushed by some Tanarukk. They backtracked them to a cave. After slaughtering all the tanarukk at the cave, they found an old note written in blood, on a tanned hide made from human back skin, that urged the tanarukk to breed furiously and build an army. A few sessions later they encountered the first ambush of the Red Hand of Doom conversion, which I had converted to use a Tanarukk army with demon support instead of a goblin army with dragon supply. When they get back to their "home town" the local lord asks for their help with Tanarukk/Troll raids on the farms outside of town. If you've ever run through RHoD, it pretty much follows a similar framework. While investigating the simple raids, the PC's learn it is actually an advanced scouting operation for a Tanarukk army. They then learn bits and pieces of the army's goal, which is to disrupt a ritual to block a planar gateway that will open on the winter solstice. This whole adventure, from 6th to 12th level, is unrelated to the big 20th level end-game.
At 12th level, after resting for the winter, the PC's had an in-town confrontation with a party of specialized soldiers from a Roman-like empire that many of them have reason to detest. The imperial soldiers are far outside their homeland. The confrontation doesn't turn violent, though it almost does. The soldiers then move on their way out of town the next day.
The PC's had shacked up for the winter with the young king they had saved and seen coronated at 5th level. One of the PC's who had recently been out buying crafting components was sitting in his room when someone snuck in and tried to steal his coin purse. He noticed, and grabbed the purse before the female intruder could do so. When he refused to give her the purse, she became impatient and reverted to her true form... a wingless Song Dragon, and breathed lightning at him, burning through about 75% of his hit points, and making him shaken. He wanted to figure out as much as he could, but had realized he wasn't going to win this fight, so he dumped the coins on the floor, and thus was able to see she was interested only in a particular coin, which she snatched and teleported away. He noted that the coin she took was a very old looking silver coin, but that's all he could remember about it (how much do you pay attention to the coins you get back as change?)
Later that same night, a shadowy figure intruded into the king's hall and assaulted and kidnapped an NPC (former player character that had earned someone's ire back around 4th level) by teleporting away with her unconscious body.
This clued them in that another former player character might be in trouble too. When they later get a chance to investigate, they find two former party members have been kidnapped by the Unseelie Court, and when the party shows up at a special location seeking advice from the Seelie Court (not understanding some of the planar interactions in play) they intrude upon the imminent execution of one of their friends by the Unseelie Court. Thus, the party gets blackmailed into two McGuffin adventures to save their two friends.
The first blackmail quest is to investigate rumors of dragons out west. They must find one, kill it, bring its body and all its possessions back and give it to the Lady of the Unseelie Court. They start shadow-walking west, and find ruins of an old city beside a lake, figuring that might be a good place to look for a dragon. [BTW - this city was destroyed due to the conqueror from 400 years ago.] Though it is a ruin, it is the largest city the characters have ever seen. There is a black dragon there, and they hunt it and kill it. When they search its body, they find several coins stuck in his scales, two of which look very old. They don't want to chance breaking the deal, so don't keep either of them, but they do thoroughly examine them first. With detect magic they learn that both coins have an invisible Arcane Mark upon them. The mark is an amalgamation of several runes all built off of each other. They puzzle out that it is a name: Hunnar
After delivering the dragon's corpse and the coins, they seek the insight of the wise women of their homeland, asking what they know of Hunnar. The wise women say they will research it while the party goes off on the second blackmail quest.
They recently learned from the wise women that Hunnar was the name of a great conqueror several hundred years ago.
The second blackmail McGuffin quest failed, so the party is on a last-ditch rescue mission to save their friend. Last night they just "killed" the shadowy kidnapper (he is a Lich-like undead, so he'll be returning later, and he knows about the cursed coins, so he'll be seeking some of those out too, and will slowly become a draco-lich shadow dragon).
Gotta jet, but I'll continue adding to this in about an hour.
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Going forward, I plan to have the party encounter one of those "Roman" soldiers, who now is a half-dragon (the soldiers were headed west to investigate the rumors for the empire, and they killed a dragon and got its coin), who became jealous and possessive, as the curse does to one who possesses one of the coins, and he killed his party mates. The PC's will find some of the things he looted from his dead friends, including the commander's written orders to search out the dragons and the coins.
The orders, and the half-dragon Roman soldier (they will recognize the armor) will be the first real evidence that the dragons are not just
collecting the old coins; the coins are
causing the recent increase in dragon activity. This will happen 11 levels after the first nebulous clue was dropped innocuously about Fafnir's cursed silver hoard, and 4 levels after the first time the PC's encountered one such coin (having it stolen from them by a dragon). They've slowly learned that others are beginning to take an interest in the coins, and they'll finally have the info to put 2 and 2 together. I can't wait to see the look of dawning realization on their faces when they figure it out.
Then, after having killed the half-dragon soldier, assuming they keep any of the things he had looted from the other soldiers, my PC's will be harassed by the Spectral Mages resulting from the other dead Roman soldiers (they were all gestalt gishes), as spectral mages can automatically sense and locate any of the items they possessed at the time of their death.
As the party starts to really investigate the heart of the dragon matter, and encounter more and more dragons, they will be targeted and harassed by the shadowy kidnapper lich-thing, who is hunting the coins for his Unseelie employer (and ferreting a few away for himself), as well as other dragons, who are searching out the coins.
[Major back-story here, some adventurers succeeded in raiding the Great White Wyrm's hoard while he was elsewhere, and by the time the Wyrm had returned to discover what had happened, several people in the adventurer's town were already transformed into dragons (the more coins you have, the faster you grow and age), and thousands of coins had left the area with merchants, etc. The Wyrm took back all the coins, save for one per newly-subjugated dragon (one coin will maintain the curse and the resulting dragon will age at "normal" rate), and has ordered them to hunt down all the coins and return them to his hoard... or else.]
There are also fiends on the loose (from the planar gate that opened at 12th level), and some of them are now hunting the coins. With the rules on Possession from FCI, the PC's might have to face the same Pit Fiend and Kluricher several times before they are actually able to kill them, and each time they face it, it will become more and more dragon-like, with the Pit Fiend eventually turning into a Hellfire Wyrm. (I plan for this campaign to go into epic levels before the players can "clean up" the loose threads created from the cursed coins).
Anyway, the big 20th level climax will be the PC's facing off against Hunnar, the Great White Wyrm.
So, there is my advice via example, on how to pace a campaign, and drop clues along the way.
Edit: I haven't updated it in a while, but you might find this insightful:
http://www.minmaxboards.com/index.php?topic=1969.0