Backing up vs. syncing

I needed to exchange my ipad so through the iCloud menu I backed it up to my computer.  Took forever, I fell asleep,later I woke up to a blank screen.  I Checked and confirmed it backed up.  Then I exchanged it. The "apple girl" told me to first update to iOS 6 then restore from my original backup and then sync it.  I did and I never got any of my videos back and nor did I get my diary program back , my app purchases back, games history and settings.  actually nothing except that contacs, calenders, notes etc EVENTUALLY synced up.  Also I should add that I have had to sync with too computers.  My laptop only has WINDOWS XP so I can't install iCloud on it.   I ve looked on both computers at the media files in iTunes and there are files for the date I backed up originally on old ipad, so I know the information is there.  Something just happened along the way.  Here's my question.......what will happen if I start all over. And what are the steps to take in what order, so I can recover my info.  If I guessed myself and didn't ask I would probably back up (just in case) then restore to original backup from my 1st ipad, then sync, then go to other computer and sync with that one.  but how does it know what info i want synced. Does it sync by the most recent infor or does it sync any and every infor it can find for any pertaining application.  Also I did start to attempt this procedure the reason I stopped was because it said iTunes will only be restoring  your contacts, notes, calenders, reminders.  So I didn't do it, cuz I thought what's the point.  So what program would be holding my diary program entries, data.  Icloud or itunes?  Please please someone help. I'm going nuts here. This has got to be the most confusing thing ever,........iTunes, iCloud. I just don't understand.  It's not clicking.  Also. My music (which wasn't through iTunes) wasn't backed up either.   Is there a way to decode those files in iTunes to see what files are backed up? 

Yes, you backup stuff from your iPad to your computer and sync stuff from your computer to your iPad.

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