I try to set the motor first, then the prop tube. Chicken and egg, really... I like it best when I've designed my own hull, and can build alignment features into the frames for a close fit. On pre-made GRP hulls, it's a bit more open as to where datums might be. In this case, I do something like:
1. Rough fit the tube through a hole in the hull with a bit of slop.
2. Make the aforementioned dummy alignment coupler.
3. Build a motor mount that puts the motor in the right place while connected to the shaft, and again with the shaft in the right place.
4. Glue down the motor mount... sometimes a thick construction adhesive will make a nice bed to set it into.
5. When that is all set, fill in the hull hole around the prop tube, locking it in place.
6. Finally, the upper end of the tube should be braced in some way to prevent it from flailing and working the epoxied hull joint.
Oh, and don't forget to replace the dummy coupling with a proper one!