Now, this is top-secret hush-hush information, and you'll have to be eliminated if you divulge any of this info briefing, but here is an IJN routing chart of the traffic in November and December 1941...
Some of the groups will not show on those routes until after January or February 1942, so this really doesn't disclose much - but it gives you an idea of where things go to / come from. That's Indo-China to the left, Hainan to the upper-left, Hong Kong in the middle of the China coast, Formosa to the top, and of course, the Philippines middle-right. Manila Harbor is lower-left on Luzon, and Lingayen Gulf is middle-left on Luzon, where you see the highly-trafficked black dots for waypoints. The "green" T thingies are US installations to induce the enemy to shoot at the shore when the invasion forces come within range, but do not actually "help" the player. That's San Bernardino Strait in the lower-right of Luzon, where you see anotheer mess of waypoint dots from the invasion forces there early.
Which submarine are you in, an S Class? If you completed the first assignment to San Bernardino Strait, you should be assigned another objective in the Philippines, not sent immediately to Java via Borneo. However, going that way, you would only encounter a few Allied ships (maybe), and minimal IJN, if any, since they are all behind you.
