Yes - the ports are assigned in the output bus definition in Administrator. You should see which port # is assigned to what extension.
Assuming everything is labelled somewhere, you should try match up the port # with the extensions on the RAP units.
Port #1 will be the left most LAF card (looking from the rear of the logger), with the top slot being #1, port #2 being the one directly below it. Depending if you have LEO's, the left LEO will be #5 and #6, and the top slot on the 2nd LAF (directly to the right of the first LAF card) will be #7, #8 and so on, with the right side LEO being #11, and #12.
If you are using a shared output bus, make sure all the port #1's go to Group 1, and Out1 goes to the RAP unit associated with extension #1, and so on.