Actually there was a submarine made for sitting on the bottom in recent years. The Soviet Typhoon, check out Jane's book of submarines and that will describe some of their abilities and characteristics.Now there you go. Later today, that knock on your door will be the FBI coming to question you on why you want to know so much about the design of modern day nuclear submarines....
But to answer your question, the same place it goes when your not on the bottom. Also, unlike the movies, subs don't sit on the bottom (intentionally). Old, diesel subs, maybe. Not anymore.
Dan
Yeah, I wouldn't worry about the FBI either, but those in the NSA, DIA, or NCIS I'd then start to worry. Signed enough forms when read out of programs that I know with the wrong then said (if found out) I could be sitting with Mr. John Walker out in Colorado.
Yes, I did eat submarine sandwiches onboard a sub. If a sub was on the bottom and someone used the head, it would still go to the same place (known as the s$!t tank) and it can be pumped or blown from a topside opening.