Both computers are using the same iTunes account but again doing a sync from the computer that doesn't have all my music and says it will delete the music on my iPhone with the sync. You can only have one iTunes library it seems, so both computers have to have the same music, video and apps if I don't want to it deleted from the iPhone.
I found this and am trying it now, so far it seems to be working:
"When you connect you device in there will be an icon with the name of the device. Click the little arow facing to the right, right click on the music pannel and select tranfer purchases and when the window opens enter you password as normal and then another window should open saying "songs are not authorized" and press Authorize"
So basically both computers will have the same iTunes data on them for the sync's. Kinda of a shame you can't just add music, video or apps without having to take up so much hard drive space on another computer.
Update:
Not all my music, videos or ringtones were transferred. So it seems this is only a limited fix.