[Bonesone4] “Is exporting to a self contained quicktime movie the best way to go?”
Yes.
[Bonesone4] “what should my export settings be from there in order to bring back into FCE to replace the raw sequences”
DV NTSC 720×480 at the same frame rate your sequence is.
If you had FCP instead of FCE, the answer would be different. But for FCE in standard definition, it only works in DV.
-Russ