You can only do it in one lump sum. This can be done either online or with MS. If you are doing it with the rewards dollars you just enter the rewards card as if it was a credit card (not sure if it works online though).
You can only do monthly with direct draft from your bank account.
Paid mine this morning with Disney rewards. As someone else stated you give them the card number just like your credit card. I unfortunatly was $25 short so had to pay the balance with my actual Visa.