What happens to the data in apps that you choose not to backup with iCloud?

Hi,
I have a 64b iPad and a lot of the storage is used up with data stored inside apps. Some of these data stores are 10s of GB in size. Such as, I keep some videos on my iPad that I play with VLC player. When I upgraded the iPad to iOS5 and activated iCloud backup, it immediately told me there wasn't enough room to back up my iPad entirely. I turned off backing up certain apps, such as VLC.
What happens to these apps? Are they still backed up during regular syncs with your Mac?

when you plug into itunes you can backup to both locations (icloud and locally) just not a the same time. When you click on your phone in itunes you'll see this option
click icloud then sync (will backup to icloud when you sync)
afterwords
click back to this computer and sync
keep in mind that if icloud has a 5GB backup limite unless you upgrade it
10GB — $20/year
25GB — $40/year
50GB — $100/year
edit: forgot to say
if you don't sync with itunes to the computer then whatever doesn't go to icloud is not backed up at all.

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