I can't believe I'm having so much trouble with this...I've had 2 iPads (original and "new") and I just can't get this right! I want iTunes to "know" which apps I have on my iPad. When I'm in iTunes and check the Sync Apps box, all of the apps are checked. I don't want all of my iTunes apps on my iPad. Do I really need to go through each app, checking to see if it's currently on my iPad or not and uncheck those that I don't want to transfer?
Also, I have a lot of my apps in folders and have them arranged on my iPad the way that I want them. iTunes wants to throw them all onto my iPad without folders...the way I have them now I have 3 screens of apps...the way iTunes wants to do it I'll have 11!!! Then I would have to go through them all and create folders and drag apps.
It seems to me that there must be a way to go from the iPad to iTunes and not from iTunes to the iPad...anyone?

With the iPad connected and iTunes open, right click on the iPad under the Devices list in the left column, then choose Transfer Purchases.

This may fix the folder problem as well, but I won't guarantee it.

Read the second post in the following thread. This will work so that the apps stay the way you have them setup on your 2 iPads.

Connecting iPad 3 to Smart TV

- Do you have an iPad backup on the computer? Go to iTunes>Preferences>Devices.
If not make a backup by connecting the iPad to the computer and right click on the iPad under Devices in iTunes and select Back Up. Make sure there is a backup in iTunes
- Transfer iTunes purchases to the computer
- Disconnect the iPad from the computer then go to Settings>General>Reset>Erase All Content and Settings.
- Then sync the iPad to the computer and set it as a restore from backup.