Honestly, I don’t ever run boundary - I have a ruler and have never had something unexpected happen. I pay attention to where the origin is in Lightburn and line it up carefully.
If you want to give it a shot, going off memory (it’s been some time) get Lightburn connected via USB, and just issue run boundary using the button at the lower right. I think it’s that easy. Don’t be tempted to run the program from there it will fail and probably in a way that leaves the laser on and stopped.
Personally, I use user origin. That matches up with the “set origin” button on the touchscreen when you start a job. Alternatively current position will start from wherever the tool currently is. Absolute coords is also an option if you want to use that so that you can precisely position something in Lightburn if you know where it should be.