As long as it is QT it should work. If not, convert to a lossless QT codec like Animation, PNG, or Microcosm.
If by "touchup" you mean paint work, then I recommend converting to a tiff image sequence. Work on this sequence so you do not accidently paint over your master clip. Working on a sequence allows you to quickly do a command-s to save as you work. Commotion has a nasty bug when painting on QT's... it will save your painted frames to the end of the clip then try incorrectly to put them back in the right place on playback. Once you are done with the clip do a "save-as" and choos your QT codec for FCE.