if i have been using my new phone for a few months and I have not set it up on the computer will it delete everything on my new phone if i restore everything from my old phone on it?

When you restore, whatever in the iTunes backup will replace whatever you have on iPhone.

Not if you carefully follow the procedure outlined in this user tip from wjosten: Syncing to a "New" Computer or replacing a "crashed" Hard Drive. If you're using iTunes 11 you'll want to first go to iTunes>View>Show Sidebar in order to follow this guide.

Edit: Sorry, didn't notice that you were restoring from the backup of an older phone. Before doing so, connect your phone to your computer without syncing and import your photos, as outlined here: http://support.apple.com/kb/HT4083, to avoid losing them when you restore to this backup. You will lose the app data from your current phone when you restore to the older backup.

Message was edited by: randers4