FEZ Domino and battery A123 LiFePo4 1100mAh 3.3V

Can I use A123 LiFePo4 1100mAh 3.3V batteries for my FEZ Domino board?

two in series should work, connected to VIN.

if USB and external power connector?

What are you asking? Can you connect these batteries in addition to USB and/or external power? Not a good idea.

If you used two batteries in series, they would connect to the power connector.