...One can define an LCU called "SubRon xx" and give it some engineers and NavSup and put it where it's needed (along with an AS). Making SubForXxFlt HQs is also a good idea, with the same compositions (but more of everything). Put SubRons under a SubFor HQ, assign ASs to SubFor HQ (and use a mental house rule that keeps them in the same area) and then limit sub operations to bases with a "Sub" unit or "Sub" HQ. Have to be a self imposed limit, but I think it will make for a more realistic appreciation of actual submarine operations from a player standpoint.
Very good idea and something worth modding into the game - I already use the mental house rule you described, I limit my sub operations to a few bases (currently, May 45, Guam and Darwin, all patrols start or end there), and I don't allow my subs to replenish at a port which contains no sub tender. Adding a few leaders which might be missing in the game,shouldn't be a problem either.
Thanks for your input!