Someone beat me to it ^^^
Use Dropbox (or similar), that way you can maintain your file structure, and file names and still have everything come out the way you want. I don't do a lot with photos but I do a lot with drawings, and I use Dropbox and Goodreader, and for me that works really well.
In fact I have a theory about this - the apps that Apple provide are really just there to give the ipad some usability out of the box. By not providing a proper desktop and file management app, Apple have left the field wide open for third party desktop/file management apps, and that is essentially what you are looking for.