I think the only way to do it is to export the hands out of one and import into the other, but I'm not sure without looking.
Check the pokertracker forum at and do a search on combining databases.
If you use PAHud, you don't even need to do that. Just do a backup of each database (assuming you use PostgreSQL), and restore the DBs to each other's computer (ie, restore his DB to your computer and vice versa--using different DB names, of course). Then, show PT where the DBs are and set up PAHud to look at both DBs...