You can use multiple vouchers to pay for your flight. Although I've personally never gone this route, the online payment system should accept multiple vouchers, per the instructions:
If you would like to use more than one voucher, you must apply them one at a time.
If you're still having trouble, book using 1-800-JETBLUE. Inform the reservation agent that you're having an issue using multiple vouchers on the website, and let them take care of it.