Yes, you will possibly need some rough cut to avoid throwing away extra work later, but generally it doesn't matter much - tracking is always done on a per-shot basis. If you have a clear idea about what clips you are going to use you can just as well start out in AE.
Thanks for the quick reply
I think thats the way ill go alright. Dynamic link seems to be behaving itself so thats a big help.
Anything involving motion tracking should start with determining exactly what portions of the shot you will need to track. I always render a digital intermediate with a good frame based codec for motion tracking. Once the required tracking is completed I build the rest of my composite and that project is rendered to another digital intermediate to use in the nonlinear editor.
Trying to save time by doing everything in the dynamic link on complex projects that require a lot different tracking operations may actually cost you time in the long run. Dynamic link is very handy for quick little fixes on simple shots. Having a Premiere Pro sequence with 50 dynamic link shots is asking for trouble.
The opinion expressed is based on my experience. You may get lucky, or you may not, but I promise you that if you get in the habit of working out your effects shots in AE and rendering them, your editing experience with complex projects will go a lot smoother.