I'm probably going to repeat stuff you already know, but here is how it should work.
Create a folder where you want all your synced pictures. Create some subfolder, one for each album you want them organized in. Use copies, don't use your original's, since you'll wan to be able to move or delete them from these albums without worrying that you'll lose something.
In iTunes, with the iPad selected go to the Photos page. Select to sync photos, select the folder where you put the pictures. I also suggest selecting to sync selected folders. That way you can easily add and remove folders later. Check all the folders you want to sync.
It's a good idea to keep an eye on the Capacity bar at the bottom, to make sure you have room for everything.
Sync.
Any changes you make to the pictures in the folders, the folders themselves, or to the setup in iTunes will happen the next time you make a sync.
To gain more control over syncing, say you'd like to go into iTunes, make changes and then sync, instead of it syncing the moment you plug the iPad in; open Preferences in iTunes, go to the Devices tab, and turn off auto-sycn.
