The best solution is to create a folder on your PC, just for the photos you want to sync to the iPad. In this folder create other folders, one for each album you want to appear on the iPad. You want only two layers of folders. The master folder, and the album folders that you will place (copies of) the actual pictures in.
When you've done this plug your iPad into your computer and select it in iTunes. Go to the Photos tab at the top and change your sync to the new master folder. If you like you can choose to sync the entire folder, or only specific album folders. When done, sync. The old photo album will be deleted and replaced by your new photos and albums.
From this point on when you want to make changes you do so in the master folder, then sync again. If you want a new album, just create a new album folder and put the new photos in it. To delete a folder, delete it from the master folder; or you can just unslect it from the sync settings if you might want to add it again later.
iOS and iPod: Syncing photos using iTunes
The other benefit of doing it this way is that the original photos are not at risk, since you will (hopefully) only put copies in the sync folder(s).