You need to ask what codecs were used to produce the different files. For instance, if the MXFs are DVCProHD, FCP will transfer these files easily. Same is true of the QT files. If they use a FCP codec, you simply copy them to your drive and import them. If both use the same codec (like DVCProHD) the files will be of equal quality.
John
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.5 QT7.5.5 Kona 3 Dual Cinema 23 ATI Radeon HD 3870, 24″ TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 2 (FCP 6.0.5, Comp 3.0.5, DVDSP 4.2.1, Color 1.0.3)
Pro Tools HD w SYNC IO, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec Monitors, PrimaLT ISDN