ITunes Sync with iPad restores deleted apps

I've thought I've locked this down, but I guess I am not understanding settings or such things. I have an iPad2 updated to latest iOS, and iTunes also with most recent update. I do not sync wirelessly. When I plug my iPad into my PC it automatically starts to sync with no problems. The part that I am trying to avoid is that it automatically reinstalls anything that I've manually deleted off the iPad whether it be apps, songs, documents, etc. . .
I am looking for iTunes to back these sorts of things up and to add changes on the iPad to the PC side of things, but NOT for iTunes to automatically restore things that have been removed from the iPad since the last sync. I've deleted a bunch of apps that I don't use and take up too much space. Same with songs and documents, but today when I plugged it into my PC, iTunes restored everything until I had out of space errors. That being said it created new pages to add all the restored apps to and now I have to go through and delete all those again. My fear is that after all the work I put into make these changes is that next sync it will repeat the same problem. Like I said earier, I thought I had made the proper setting changes, but apparently not.
Any help is appreciated,
Thanks!

It has always been very basic to always maintain a backup copy of your computer/files/docs/music/pics/etc.
Use this to put everything back on the hard drive.
The ipad syncs with one library. When you installed a new hard drive, the it became a new library. The ipads content will be erased and replaced with content from the new library. That is the way it works. Another reason why you should use your backup copy to put everything back on your new hard drive.

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