On the issue of crew configurations, I agree with akdavis - the default starting crews are way off base and need to be adjusted. This was a quick and dirty setup I made for the 1944 Balao:
This crew setup assumes there were two petty officers for every three seamen and no more than 4 CPOs (would have to get rid of the CPOs on the AA and deck guns and move at least one into the Control Room). Balaos had up to 10 officers, two of which would be Ensigns straight out of the Academy who were not an official permanent part of the crew but nontheless would go on "familiarization" patrols with the regular submarine crew (the same way the Kriegsmarine would send officer cadets out on U-boat patrols). For our purposes I think having 6 officers, all in the Command Room and on Deck Watch is fine.
WRT to crew lists, this is what fleetsubmarine.com lists:
Balao: 10 (officers); 70 (enlisted)
Gar: 6 officers, 54 enlisted
Gato: 6-10 (officers); 60-70 (enlisted) Crew size increased as war progressed.
Porpoise: 5 officers, 49 enlisted
S-Class: 4 officers, 34 - 39 enlisted
Salmon:5 officers, 54 enlisted
Sargo: 5 officers, 54 enlisted
Tambor: 6 officers, 54 enlisted