One trick i found while poking around is to "merge" traffic files from campaign folder into my current mission file. Just be sure not to check the "save merged' box or you'll have big problems.
This allows you to place your ship traffic in a way that doesn't interfere with the default traffic.
Another great help is the merge the "Campaign_LOC.mis" file into you mission file. This will display all the port layouts so you can start at the right dock if you wish.
I.E. i merged "Campaign_LOC.mis" and "US_HarborTraffic.mis" and was able to see all the harbor docks and docked AI ships so was able to place my sub right in the exact spot i wanted...
-ew