Personally I just add the price of a masterwork club, mace, or whatever it happens to function as to the price of the rod (including any seperate magical enhancements). Otherwise using a non-weaponized rod as a weapon is just an improvised weapon, probably equating out to a club.
It is added on with no surcharge, so you can have a +2 Flaming Mace/Rod of the Sandwich Summoning.