Yea, adding cherries to the bottle dosn't sound too great. kahuna's suggestion will work fine I bet, just beware that the berries take up alot of volume when you add them, and on top of that, expand and bloat due to gas. I thought i read about someones attempt at the same thing, but he said that most of the cherry flavor was lost. good luck though, sounds like a tasty idea.
Primary: blueberry apple cider
Secondary: panty dropper cranberry apple cider
bottled: I should probably get some of those...
on deck: future brews suspended for the moment :(...