As recommended by one in this thread, you should use Google Sync. It's just easy to store the data in the cloud and then it's easy to move between devices especially when you upgrade to other devices. You can use it for calendars as well which can be handy.
if you have everything on your phone now, when you dock next time you just choose to sync contacts with gmail/google. It'll say something about preserving existing which you want. Obviously, you will need a gmail account. After you do that, then you can shut off the iTunes sync and just use the over-the-air google sync. So if you put a contact on the iPhone, it'll show up on the iPad within a few seconds automatically.
Just read up on the google sync site. Gives all the details so then you don't have to be tethered to a PC with the syncing or worry about loosing with harddrive failure or anything.