I'm lucky - my cross slide handwheel is marked in 0.5 of a mm divisions which makes life slightly easier on the math. The hardest thing is accurately setting the work so the cutter is "just kissing" the surface of the wood before turning the dial on the cross slide the requisite number of times before you start cutting the thread. "Just kissing" is much easier to achieve with a very hard wood like box than with a softer wood like sycamore as the points on the cutter are very sharp and the kiss can easily become more intimate (if you see what I mean) - which means you then cut the thread too deep :-(
As to getting the parts you want to thread cut accurately - I know exactly what you mean. When I make a threaded box, I make a plug gauge to fit inside the lid recess and measure the plug gauge as a starting point (I have not found a sensible method of measuring inside a recess in wood accurately and repeatably enough), then add the requisite number of mm for the size of thread I'm cutting to this and cut the flange on the box to that number as accurately as I can - which means a lot of stopping and measuring as you near the correct diameter!
The key I've found is to follow exactly the same procedure each time - and I tend to make threaded items in batches of 10 or so, as I find I get more accurate the more I do.