we use Auto Duck nearly everyday, I feel it is a really handy utility … It will link AE directly to the captured clips, so there is no re-compressing. It will replace your dissolves with opacity keyframes, scaling, position etc etc … I generally just use the motion effects as guides in FCP then re-do them in AE as I find it easier to use.
You will find some things don’t tranlsate so well with Auto Duck …. like text will come through in a different font … timewarping/reversing sometimes seem to comethrough differently … after a bit you will know which things need to be double checked…. sometimes it will interpret the footage incorrectly …. all easy fixes, just things to check..
you don’t need to finish in AE .. in fact, if you are working on anything long its probably better not too. . just do your effects shots in AE …. you just need to make sure you use a codec that is lossless … QT animation or such,,,,
hope this helps …