Ahoy Jangles
1: This depends on what UI you are using. There should be a depth bar/gauge you can click for specific depths to 25m. Holding SHIFT will change that same bar to "deep depths" so you can choose depths to 250+m.
2: You can ask your CE to use ability "reduce flooding time" and if his morale is good and he is not injured he will comply. Other than that, and maybe being at battlestations and also using his "more crew to damage control" there is not much more you can do to battle flooding.
3. This might not be the latest version but it's the best.
SH AI Explained
It's for SH3/4 but trust me all the basic principals are the same.