How to manage data folders?

GE is working out great, except for the data folders. Each time I make a new game, it picks the data folder itself from the previous data folders (it almost seems random)...is there any way to change this? Some of my games' data folders have EVERY graphic from EVERY game in them. Makes backing up, or posting demos here nearly impossible, as I'd have to sort the 45 mb data folder each time. And of course if I delete any images from a data folder...some game won't load...and you know how long it takes to attempt opening and correct missing files one by one like that?