Welcome to MobileRead, badspell68!
I'm not entirely certain that I'm following what you're asking about, so If this answer seems to be totally off, that's why.
When you put a memory card in the Reader, it searches the whole card for any file types it recognizes (that's the spinning arrow thing). When it finds them it will simply add them to the list of files: pictures under pictures, audio under audio, and anything it sees as books under the list of all books.
They won't be in any sort of category or anything (unless you use the eBook Library software to build categories on the memory card), but they'll have a little icon next to the name in the list to indicate that the files that are on the card (it looks like a little memory card, unimaginatively). If you have a file on the card that isn't showing up under the all books menu, then there's probably something off in the file. That's not the only possible reason, just the most likely one.
One note about PDF files, in case you don't know this already, if they're formatted for a letter sized "page" they'll be pretty much unreadable in on the Reader. Once a ~14" diagonal "page" is scaled down to the Reader's 6" display, it's just too much shrinkage.
If, however, the PDF's "pages" are formatted the same size as the Reader's display, they work quite well. The only hazards there are that big files can have some problems when they get above page 1,000 and page turn speed can be a bit slow.
Hopefully that answers what you're wanting to know. If not, ask again and we'll take another swipe at it.
