I found Cutty, and now I need to find an evidence box upstairs in the captain's quarters. How do I get there?

It is either in one or all of the cellblocks that there is a stairway or a door leading up there. I also think there is a secret passage behind one of the guard stations that gets you there.

Sorry this is a really vague answer but I haven't played in so long lol.

I think it's location changes depending on the difficulty setting you are playing (I only play on Expert so am not completely certain).

On Normal difficulty it is in the Officer's Quarters. On Expert difficulty, it was stolen and was taken by a thief who hid it in a hiding place near the watchrooms.

http://www.thief-thecircle.com/guides/keeperchapel/Cragscleft/

Keeper's chapel walk-through for the level. It should tell you all you need to know.

Ok I've played the mission again now. The stairs out of the prison are in cellblock 1, if you check the map you can see them top right corner of the cellblocks. Then take another set of stairs up inside the chapel. The secret passage I mentioned is actually where you have to go on expert to get the evidence (after finding it's not in the safe like usual) and you find it at the guard post with the flashing light on your way up to cellblocks 3+4 - there's a hole in one of the walls you can crouch through. Note it's not jumping into the flowing water, that leads to the bottom of the mine and is a handy way to get most of the way back out..

I do have a feeling there is another secret passage somewhere that goes up to the officer's quarters but I really can't remember for sure. There is a secret room behind one of the banners you cut with your sword up there with some wine in it and I *think* it might be in there but I spent a few minutes and couldn't find how to open it so maybe I'm remembering wrong.