Converting MTS files help pls!

Ok I have found out media encoder converts those dreaded stand alone mts files great news. So the footage coming into encoder is avchd 1440x1080, they are big clips averaging 20mins each.So my question is I am doing the edit in fcp6, should I encode them as apple pro res 422 or H.264? Secondley, the client wants a exported video for youtube 1280x720 should I change the frame size in adobe media encoder or when i export my final from fcp 6?

Thanks in advance!