There should probably be a general discussion thread labeled here... Because it's confusing to have a subforum without a specific general thread.
Some of my general thinking:
The Totem Chakra is for copying existing things. It's taking on traits of other things on a deep level, but it's drawing what's outside into yourself. A Totem Chakra Dragon class is akin to the Dragonfire Adept, drawing on external things to change themselves into a more potent form. They can change what sort of draconic traits they are using on a day to day basis, as they aren't tying their being to one particular thing due to using Incarnum. The Dragonfire Adept, itself, doesn't bind itself to one particular type of dragon, instead calling on many draconic traits as desired to deal with the problem.
The Soul Chakra is for what you are inside. The core of what you are, not what other things do. Drawing out what's already in you. A Soul Chakra Dragon class is more like the Dragon Disciple, gradually becoming a draconic being from calling out what's already in them. They don't change all their draconic traits on a daily basis, having their energy type locked in place from the first level due to forces outside of Incarnum use. As with the Dragon Disciple, the type of dragon is fixed, the traits are all tied to this one thing.
In both cases, the Dragon Incarnum class focuses on breath attack use, as well as getting access to other common draconic traits. The Soul Chakra class would have some features, such as Energy Resistance, be class features rather than Soulmelds, tied to the energy type at first level. The Totem Chakra class, instead, could become a mixup of different energy types and mechanics from Dragons with no properly coherent theme.
As for how to set up the things for the dedicated classes, I've had ideas for Undead-themed Incarnum classes that do center on Necrocarnum, but not solely the Zombies. Admittedly, one of the ideas is a class dedicated solely to Necrocarnum Zombies, but that's a matter of keeping to set of three classes for it.
One of the ideas is having the class dependent on external sources of Essentia. Essentially using the souls of others to power their soulmelds, rather than the force of their own. One of the things I can think of to mitigate the strength of this is to have added requirements and penalties to using this, with some high-power Soulmelds requiring this extra Essentia. The fluff on Necrocarnum is that it's a twisted version of regular Incarnum energy, which I take to mean having the typical positive energy of Essentia replaced with negative energy, which is hostile to normal life. So something like -1 Con per Necrocarnum Essentia you have would work out as a limiter, with a means of getting your Soulmelds Charisma based later on, as well as Charisma to HP and Fort save. Meaning that, at high levels, your only use for Con is avoiding death-by-zero-Con. Include an Undead transformation and that stops being an issue.
As for Soulmelds, the name of the game here is Touch-attack effects with clauses for Natural Weapons that some would grant. Temp HP based on extra negative energy damage dealt, Con damage, Dex damage, Wis damage, Energy Drain, poisons, diseases and so on. With Necrocarnum Zombies getting a chunk of the list based on type of undead being made and Soulmelds to give buffs to them. Ideally, you'd be able to switch from Minionmancy to an unarmed SoS build, with doing both being possible, but unwise. The Chakras give a wonderful ability to balance things by giving slot contradiction, so similar features for Minionmancy and the natural attack setup(Claw/Claw/Bite for two Soulmelds with inbuild minor riders to get it started)
Oh, also the Necrocarnum Essentia being tied to Chakras. Fluff-wise, it's tying masses of Necrocarnum Essentia to the Chakras for long-term stability. I'm thinking that the mechanic can be extended by having it so that there'd be Gravemelds that get half-effect from regular Essentia and full effect from Necrocarnum Essentia, with regular Soulmelds getting the reverse, adding an additional build choice by having the character choose which side they want to focus on. Regular Soulmelds being mostly the minionmancy, Gravemelds being mostly the natural-attack setup, with a rule stating that at least half the Necrocarnum Essentia on a Chakra would need to be invested in the soulmeld(s) shaped on that Chakra. So sticking Necrocarnum Essentia onto a Chakra is biasing you towards using that slot for Natural Attacks.
TL;DR version: Class feature to get alternate Essentia type, permanently bound to a Chakra, giving -1 Con for each point you have, that works normally for class's special Soulmeld category, while being half effect for regular Soulmelds. Regular Essentia having half effect on special Soulmelds. Special Soulmelds being focused on personal Natural Attacks with various on-hit effects based on debuffing the opponent into oblivion, regular Soulmelds being based on making and improving Necrocarnum Undead. Class features for Cha-based Soulmelds and replacing regular Con functions with Cha, coming in throughout leveling.
For the class's Chakra, it'd be Soul, due to gradually becoming more and more Undead and making it so that they are internalizing the stuff all the way down. Right at the level of getting the Soul Chakra, they'd get Negative Energy Affinity, making them Undead in every way but creature type. As in, including many of the immunities, like Poison and Disease. Basically all of them except immunity to non-object Fort saves and mind-effecting.
I also have considered Incarnum item crafting, and think the ideas I came up with for that to be a good spot to start for a Construct-themed Incarnum class. The two main ideas I had were Soulmelds improving other Soulmelds and variations on Incarnum Weapon that make different items for the equipment slot they are bound to, with simple Shaping granting an effect to whatever item of that slot you are wearing, with the item slots in question being much more limited than the number of Chakras, to make stacking possible.
For example, let's say that you have crit-range increasing, throwing distance boosting and added Dexterity as Hands slot binds. Binding the critical-range increase creates a Scyth, a nat-20-only crit range weapon with a x4 damage multiplier on crit. Binding the throwing distance increaser creates one Light Hammer, 20 ft. throwing range increment, or Throwing Axe, 10 ft. throwing range increment, per invested Essentia that reform in your hands at the start of each round. The Dexterity boost, when bound, would create a Kukri or Shortsword. All with an Enhancement Bonus to Attack and Damage equal to invested Essentia. Essentially, Binding the Soulmeld creates a weapon, or weapons, that is useful for the effect provided, including being a weapon that becomes useful through the Soulmeld.
As for Soulmelds that upgrade other Soulmelds, it'd be a category that explicitly can be shaped to a Chakra without actually occupying it, providing it's effect to other soulmelds shaped/bound to that Chakra. The Binding effect would be to allow another Soulmeld to be bound to that Chakra as if it were a different one, such as letting Arms binding effects be applied for binding to Hands, and Shoulder effects for applying to Arms. Basically letting you turn one Chakra into another. Naturally, Split Chakra would allow you to buff two Soulmelds at the same time with one of these, working around a major limiter of Soulmelds for two of them.
Associated items wouldn't be just copying the Chakra/Item Slot relation. Instead, Hands/Arms/Shoulders would be for things you hold in hand and wear on hand, being gloves, weapons and shields. Feet/Waist/Heart would be for the torso and below the waist, meaning that any of the three could be armor, belts or boots. Binding armor to your feet would be perfectly doable. Crown/Brow/Throat would be for the head and neck area, and covered in overlapping effects of the AoE sort, with the need for a Bind to make the thing you are using, but merely Shaped ones could be allowed to stack it. Of course, there'd be overlapped wording for certain hands/arms/shoulders Soulmelds that give splash weapons, which just means you can get weirder with your crafted nonsense. And Spiked Armor and wording for Shields could allow for shenanigans with defensive properties.
As for minion-making, I'd have it be directly Construct based. Such as a shaping making you functionally have bonus Construct HD in the form of temp HP and bonus to-hit, with the Heart Chakra Bind effect being to make ML Constructs with E HD, each with your armor-bonuses. Or a Shoulder Chakra bind making an Arbalester with your weapon bonuses, with the Shape effect being instant weapon drawing and reloading. And part of the situation is being able to hand certain 'Meld-made items to other players, such as arrows that replicate your other 'Meld effects, limited to Essentia invested in the arrows and the other 'Meld.
TL;DR version: Soulmelds in three categories, each with three Chakras to the category, and each category being creation of a type of item for the Soulmelds to affect/make. Hand/Arm/Shoulder for hand-held/worn items, shield-based attacks being included as weapons. Foot/Waist/Heart for boots and armor, with boot-bind effects being mobility and defense effects going to armor-binds, while the Crown/Neck/Throat chain is for blatantly-shenanigans AoE and mobility effects.
For the class's Chakra, it'd be Totem, due to the internalizing of magic item effects and basic Elemental force directing. Totem Bind effects would largely be for increasing effect stacking options and saving space from the really simple stuff. Like, instead of having Soulmelds that directly give you AoEs of the basic damage types, those effects would be rolled into the basic damage adder of the same type.
So... Thoughts on the basic ideas of these two class ideas? I'll wait for comments before doing another idea pair. Probably being Ooze and Dragon, to be honest. Or maybe more intricate ideas for guidelines on Soulmelds to use for guiding my attempts at working out a new class for each. Probably including plants, to get the sort of coherent design philosophy I'm going for included in it. More likely to be AFCs for Green Man to work mechanics differences, followed by Soulmeld set for design philosophy compliance.