It's dead easy.
Place the port as a new base same as you would an airfield.
Place CVTG as a new base. (At least 3 miles from any coastlines)
Save and reopen terrain.
Highlight SHPxxx000 (The CV) of the TG you just placed.
Double click its entry in the Selection list.
Enter the base number of the port in the drop down box next to the 'group ID' box to 'bind' it to that port.
The save and reopen is to get the port showing in the last step, the port base number will not show unless you do. You can then set the default waypoints with the Task Groups tab. If at any stage something looks like its not working, save and reopen the terrain. This usually solves a bunch of stuff.
Gatso