First I'm importing the raw images into iStopMotion, do some first polishing by removing unnecessary frames, import the iStopMotion-project in AfterEffects (it's an uncompressed .mov-file), remove camera shaking with Tracker Controls, export into uncompressed Quicktime again, import the polished footage into FinalCutPro and apply the SmoothCam-filter, so that my video has as less shaking as possible.
The editing process is also done in FinalCutPro, because I'm used to edit videos with this, instead of Premiere, which happens to crash on my Mac anyway (usually while saving a project

).
Since I'm shooting in a non-chronological order it makes sense to split the work into scenes, so that each of the 20 scenes gets this treatment.
But my tripod is a cheap pile of crap, so even after all of these optimizations there's still a little shaking left...