Range from base to patrol hex:
This has 2 effects, the delay getting to the patrol hex and the delay getting back home. I have not seen any other way the range has effected subs' performance. Best thing is to base as far forward as possible, and you DON'T have to worry about losing the subs if your advance base falls to the enemy, because the subs are already "on patrol". They will automatically get a new base assigned. Look at the new base and if you don't like it, re-base the sub again. Also ad DadMan says, the close you are to emeny air bases, the morelikely you are to get spotted, This always lowers the effectiveness of the subs. I still routine place a "patrol line right outside of tokyo, nagoya, etc. It's always good for a few turns, then I move it.
Loitering in a patrol hex:
Move the subs EVERY 2 turns. Contrary to the rules, there is no "down time" if you move the sub unit to a patrol hex that is close enough to its prior patrol hex (probably if distance <= speed, no delay). I just "shift the line" the first sub moves to a new "good spot" while everybody shifts down along my "patrol line". If you don't move the subs, and they get spotted (no indication by looking at the sub) its effectiveness will diminish rapidly.
Finding the "good spots"
Set the display to high and delay to med or long when the TF return phase starts and / or when the Japanese routine convoy phase starts. This will show your the "routes" being taken, and you can see your subs in action (and you can watch all the Mark 14 torpedo "duds" too

Sub Types:
I never had much luck with the S class or the Dutch KXV class subs. All the other US class subs seem to do fine, but watch out for the early types, Salmon, Porpoise, etc. I don't think there are any reinforcements for these classes and I often get down to 1 or 2 subs per unit

Sub Damage and repair:
I never see any damage indication on subs on patrol. The game must automatically withdraw damaged subs from the patrol group, and add them back in some undecipherable manner, because I never see any subs in the ship pool.
R-organizing sub units:
Not necessary unless a few groups get hammered, ie many losses. In that case you have to return the sub group(s) to port, along with an "overstrength" group or two so you can "equalize" the sub groups" using the old reliable to pool and get pool options.
Sub Computer control:
Not recommended, because the AI will not place the subs in good locations, and will not move the subs often enough. You'll have much more fun doing this yourself.
