I would advise downloading my GONE ASIATIC mod;
http://www.subsim.com/radioroom/down...o=file&id=4358
And start a new career. Dunno where you read about "neutral" ports, but in the game you have one home port and several resupply ports, all indicated by an anchor icon;
The one with the tilted anchor (Brisbane in this pic) is the current home port, any of the others are ports where you can resupply, but not end the patrol. My mod adds two "secret" resupply bases in the Philippines available throughout the war.