The SynthEyes team have posted a few tutorials showing the workflow between tracking in SynthEyes and After Effects. This includes some methods for dealing with lens distortion, with some back and fourth.
Russ Andersson starts with the very basics of tracking a shot with the Andersson Technologies’ tracker, and exporting that to After Effects where you can add some floating text layers based on the SynthEyes solve.
two-pass lens distortion workflow, which allows you to composite 3-D effects over the original footage
Russ then has a look at how to deal with lens distortions in that workflow, covering a one-pass and a two-pass lens distortion workflow. The one-pass workflow nearly removes the lens distortion, while the two-pass will allow you to composite effects and elements over the original footage with the lens distortion put back in.