I'm syncing my iPhone and iPad on the same PC too, and they both have their own list of apps. So that's certainly possible. If I remember correctly, I had to disable 'automatically sync new apps' in order to prevent any new app to be installed on both devices. It's a long time ago I did it, but I remember it didn't work as smoothly as it should. But, then again, it maybe does now...
In order to upgrade, I would follow these steps:
1. Plugin your iPod, and disable 'automatically sync new apps' on the 'apps' tab
2. Plugin your iPad, and make a backup
3. Upgrade firmware
4. Restore from backup
5. Use right mouse button on your iPad's device name (in the left pane), and choose 'transfer purchases'. This will transfer all you apps to your PC.
6. If not checked already, make sure 'sync apps' is checked in the 'apps' tab. Also, disable 'automatically sync new apps' on that same tab
7. If iTunes tells you that it will remove certain apps from your iPad when syncing, cancel it, and use 'transfer purchases' again (don't know why, but I needed to repeat this step until I didn't get that message anymore)
8. Sync your iPad
Now, please bear in mind that this is how I remembered it, but I strongly suggest you google it beforehand in order to prevent anything going wrong.
Hope this helps
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