Any Ideas on Apps to Transfer PDF collections?

Greetings,
I have a bunch of PDF files I would like to distribute to Field Staff. Many of the PDF files are organized together in subject matter. Is there anyway I can "pre-configure" and organize this PDF collection in a single file then have the field staff download from my company server? Then, when they would transfer to their iPad, the PDF's would still retain the pre-configured organization. Similar to a comic book reader app (like comiczeal), I want them to have the collections by subject matter all ready to go for them when they open the application to read them. No way they can import hundreds and then it is up to them to organize. Obviously a free app would be best.
Thanks in advance!
RC

I can't answer this very well for iPad in the Enterprise but for my personal collection of PDFs, here is something I do:
iBooks syncs PDFs from iTunes. IBooks will let you sort PDFs by category, just like it does books. The categories are the genres you give to the PDF files in iTunes. The default genre for PDFs is an empty field so normally there are no categories for PDFs but you can create whatever genres you desire for them. If you select a bunch of them and "get info" you can change the whole bunch at the same time. These genres will give you one level of organization in iBooks, and then it is alphabetical within each category.
One note, though: I have noticed that if I have already synced a book and then I change the genre in iTunes, it won't sync that genre change to my iPad. I have to unsync the book(s) then re-sync them.
Actually, one more note: As far as I can tell there is no way to collapse a category in iBooks to hide all the PDFs underneath of it. A list of hundreds of PDFs might require some scrolling to get to the categories near the end.
Maybe something in there will lead you to a simple and free solution for your staff to sync PDFs.

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Any Ideas on Apps to Transfer PDF collections?

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