Why would you want to use Boujou with after effects? Boujou is one of the best 3d trackers and would normally be used with somthing like Maya, 3Ds Max ect. Now you could use it to export data to after effects, but with After effects not being 3d, it sort of defeats the point of using Boujou. More then lickly you can get the track you require with Mocha inside after effects.
What are you trying to track, and what are you trying to do with the tracking data?