If you want to know how a sub submerges, the effects of the various controls, and the problems involved follow this link.
http://www.maritime.org/fleetsub/chap18.htm#18A
If you are going down to periscope depth for firing balancing the trim and speed of the dive is important. a steep dive will get you underwater fast but the time it takes to balance the ship for fighting trim will be a lot longer.
So far I have finished setting all the numbers for each boat's draft and I am testing everything I can think of for adverse effects. I have already established the baselines for the stock game and RFB. I will soon be done with the Salmon class tests when I finish several runs at 10 knots until the boat runs out of fuel to make sure I haven't affected the range. The dive times are close enough when taking into account the height difference. I cover the same distance over time at several different speeds, so I don't see any problem there.
I have looked at the Salmon from several angles at flank speed in a 14 meters per second wind and every once in a while the rear half of the rear deck is under a wave. It looks right when compared to the pictures I have.