Restoring iPad, copying files, etc.

I had some issues with my iPad (1) and, though I was able to fix things, I really think a full restore will help.  I also have a lot of extraneous videos, music and other docs on the device that I'd like to back up and get off.  Right now, it's only got a few gig free (32Gb model).
When I first got the iPad last year, I never really aggressively backed it up or synced it with iTunes.  I made sure that I either had files in other places using Dropbox, Goodreader or iWork.com.  For music, I manually moved things back and forth from my MBP to iPad and vice versa using iTunes one way or 3rd party apps like Xilisoft or iPhone Explorer.  (Yeah, I know all the worst ways to manage data.) 
Well it's time to do this right.  I want to wipe the device clean, reinstall all the apps, etc.  I see that the apps are sync'd up b/c they show up in iTunes.  The only thing I'm really not sure of are the files from Goodreader, Keynote and Pages.  It seems to me, that I should be able to get iPad to sync up and it will copy all of the files I have in Keynote and Pages on the device to iTunes on my desktop.  But I'm confused.  I can "Send to iTunes" from my iPad while it is connected, but where are those files when the iPad is not connected?  Do I have to manually "Save to..." in iTunes and copy them over? 
Thanks in advance...sorry if I'm setting a bad example!
Lee

Pages will handle your doc files. I use Goodreader for PDF files. Also Airsharing HD will open any of your files that you upload/copy to Airsharing.

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