The fact that the landing site will be flat and have few rocks got me wondering how we will pinpoint Phoenix's location from orbit. I know the high resolution camera on MRO can spot it, but the problem is finding it. With no likely landmarks near by, could the 3 orbiters find the exact location using the UHF signal from the lander?

Yes, the Doppler shift of the UHF can be used to locate landers. This was planned for MER using MGS but never needed, see:

http://www.msss.com/mer_mission/finding_mer/