Right now you are limited to using the existing port objects. In many cases, the most realistic pacific harbors are had by deleting what is in SH4 and having none at all.
You open Campaign_LOC.mis with the editor and under tools check the map location edit box.
Make sure you save the mission as a standard mission (ignore player sub checked in proporties). Use a copy, too, it's easy to erase by mistake
tater