I had my GBA covers printed at Kinko's for $0.99 each. They look pretty slick, but they're not on glossy paper.
Another poster on TCP noted that his Kinko's wouldn't print the covers due to copyright concerns.
As for getting the GBA manuals inside of the DS cases, yeah, you have to modify them, but it's super-easy. I'm going to post some pics later (someone on the Nintendo forums asked), but basically, on the left side of the DS case, toward the top about a quarter of an inch from the very top is a line of plastic that seems to go across for no apparent reason. Cut it out (carefully, of course) and presto!