Most threads have an undercut at the end of the thread where the tool tip should be when you stop the spindle. Since you have a brake, that is a good way to stop in the right spot. I have a VFD on mine with a fast deceleration time and it stops in less than 1 rotation when I shut off the spindle. If you don’t have an undercut, you need to stop in the same spot each time, or when you get deeper into the thread and run a bit past the last cut, you can break the tool tip by cutting too much.
The undercut should be slightly deeper than the minor diameter for an external thread, and about 1.5x the pitch. That should be enough room to stop the spindle without crashing into a shoulder unless you are going really fast. For your first threads, you might want to make it wider until you have more experience.
For metric threads, stop the spindle with the tool in the undercut, retract the tool, turn spindle in reverse to your starting position, move the tool back to the correct depth for the next pass and then run forward to the undercut. Repeat until you are at the correct thread depth.