The stern anchor wasn't used for the last few years because it became so slow to deploy - basically as it was used so infrequently, it got seized up, as well as the cable getting tangled regularly in the chain locker. I think I recall it being used in St Thomas in about 2004 (scrub that, I've seen the picture now - it was used then!), and I also think one of the 'new' Captains tried it in 2006ish despite our protests - after all, he knew best! After an hour or so of trying, we gave up - I don't even think we got it as far as the sea bed. I don't recall using it any time after that.
The windlass for the stern anchor was on 3 Deck aft - horrible place! Going back to a previous comment, the markings are done in shackles. 1 shackle is 90ft, or 27.5m. Each shackle marker is painted red, then the corresponding number of shackles painted white either side. The bell is rung for each shackle that passes on its was home, when the anchor is 'aweigh' the bell is rung continuously. This is the time the black ball is taken down, as the ship is now technically underway.