Trial and error and each pen may be different. I usually press a little and check, and repeat till I get it to where I want it. Just don't go too far. They are a bear to get out. As far as how far to stick out, far enough to write, but not too far as to look awkward. I don't measure them or anything.
I put a little piece of masking tape on the tranny about where I think I should stop. It helps me judge how far I'm pressing. Once you get one made exactly how you like it, get out your calipers and measure the overall length with the tip retracted. Cut yourself a spacer that exact length and put it in your press. Now it's impossible to press too far.
Make a u shaped block of wood that is just the right length (in your opinion), then put the pen in the U and push trnasmission down (with press) until you hit the wood block. This way they are all the same. NOW, if the nibs were always EXACTLY the same, this would work perfectly. It doesn't. But the variance is within MY margin of error since the length is a matter of personal preference anyhow.