Here is how to Edit Existing docking ports for ships in the XTC mod.
After installing the X3 Editor 2 you will need to locate the CAT file that contains the "Dummies.pck" File. In my instance it was located in 15.CAT
Once you have located the Correct CAT file with the "Dummies.pck" file (usually the highest numbered CAT file with a dummies.pck file in it) you need to open up the Dummies File with the TDebugger option when prompted.
Now that you have the File open you are ready to change the properties of the defined docking ports, for all ships that use the m6 or ts docking ports we can easily swap them out.
Select the Docking port you want to edit, and then simply change the ship docking flag to match the class of ship(s) you would like to dock in this slot.
As mentioned above you can find all of the flags on THIS PAGE.
Finally all that is left to wrap up this change is to simply save the Dummies file over itself allowing it to overwrite the existing file.
(Remmeber that any changes made WILL NOT EFFECT EXISTING SHIPS in the game, you will need to Perchase/Spawn/Cap a new one after the engine has had time to create the new ships.)