[QUOTE=Zebra]
How do you deal with the lack of sunlight and your sense of time?
Do you sort of lose your circadian rythm?
Does the sub really switch to all red lighting like your developing film during a drill?
[/QUOTE]
You deal with the lack of sunlight by going into a profession where you can be outside as much as possible once you get out of the Navy. Also, you insist on a desk next to a window. 
Circadian rhythms get screwed up more than you can imagine. A typical watch rotation is 6 hours on watch, 12 off. However, during your twelve off, you have your normal job to do as well. There are all-hands drills every day after lunch, and training every weekday morning for those not on watch.
A typical rotation goes like this:
Day 1:
0600-1200: watch
1300: all hands drills
early evening: get some sleep
Day 2
0000-0600: watch (all night)
0700-1130: training
1130-1300: skip lunch, sleep instead
1300: drills–wake up to sound of general alarm
1800-2400: watch
Day 3:
0000-0600: SLEEP
0700-1130: training
1200-1800: watch
Day 4:
Same as Day 1
In between the watch schedule, as I mentioned, you have your normal job to do. Admin stuff for officers and chiefs; maintenance for junior enlisted.
You also work on quals in your free time. However, there’s not a lot of free time. God help you if you relax to watch a movie, and are behind in your quals. Until you get your Qualification in Submarines, you’re behind in your quals.
The above schedule is screwed up even more if you are at battle stations or section tracking party. During battle stations, all hands are up. Section tracking party is like battle stations for the people whose battle stations are in the control room. I’ve had those go on for weeks. You might find yourself at your battle station all day, then have to take the midwatch all night.
Yes, subs rig for red at night, and rig for black when going to periscope depth.