Do you have the SH3 Mission Editor guide? SH4 ME works the same, it's a good guide. There may be a SH4 guide too but I've always used the SH3 PDF when using the ME.
I find hand editing some things easier and just use the ME for lat & long numbers, placing docks and bases etc.
These links may help:
http://www.subsim.com/radioroom/showthread.php?t=158234
Your problem not having a tilted anchor Home Port is probably something simple. Pearl is always a home port to its subs throughout the entire War and would be a good model to follow to set up your PT Boat home port.. Just change the location lat long, the departure points, and the Flotilla of course.
This is in:
Data\Campaigns\Campaign\Campaign_LOC.mis or USNavalBases.mis depending on what type of port it will be. Also edit the Flotilla's and CareerStart upc's to include your PT boat bases and home ports.
Edit: looks like
propbeanie and I were answering at the same time.