I'm thinking that that's just straight up in a pot, not in water.
Just to keep on this PSA safety train, beeswax should never be melted over direct heat. So it should either be melted in water, using a double boiler/bain marie, or in the microwave in short bursts.
Besides, I started with some nasty brown comb first figuring I can't hurt it.
Don't be surprised if you don't get much from the very dark stuff. A lot of the gunk in that comb falls into the "unmeltable" category.
And how long should I cook this for? How do I know when I've reached 'the end'?
Basically you just need to get to the point where everything that is going to melt is melted. Which probably isn't very helpful.
The cheesecloth will kind of flatten out as the wax melts out and leaves room inside the mesh. The melted wax won't be very visible in the water, especially if you don't get much. In the Crock Pot, it usually takes me several hours, but I'm melting a lot at one time, so it just kind of depends.