When you pay with a credit card, you can choose how much you want to pay (although, the full amount is pre-chosen for you). If you don't pay the full amount, you can pay the rest later (preferably before the due date).
I'd you use autopay, it will charge the full account balance. Manually paying, you can pay your line with your card and the rest can be paid with another card, cards, autopay, etc.
As mentioned already, you can make a partial payment but I believe if you want to use another card, you'd have to set that up through your MyT-Mobile.com profile.