I too am not familiar with the Fostex, but I am assuming that most of the hardware out there works similar. (Basically the same technique, maybe different knobs,button, etc...)
I use a Digital 10 track, and I do basically what your described. I transfer my projects to Sonar/Calkwalk to tweak/adjust because it is easier for me to see what each track is doing .(As opposed to just hearing it)
Anyway, I transfer via USB. Once I have laid Drum Tracks, I transfer it. Bass Track, Transfer it to a seperate track, and so on and so on.
When I get to the vocals I do the same thing.
I guess my answer to your question is my setup won't allow me to transfer tracks as a whole, and it copies in Cakewalk as individual tracks. I have to transfer each Track to an individual track via USB to be able to control/adjust tracks on PC.
I hope I didn't confuse you, but I find that way of recording more fun and easier to control. Although some may say it is time consuming, I enjoy it!
One Love
Trizza