Make your life easier: mill a shallow pocket into your wasteboard slightly larger than your circuit board. It’ll help you position and clamp/tape your board in place and keep it square to the machine.
If you’re going to be doing multiple separate toolpaths, such as a drill before a trace routing, you need to give yourself a registration mark to keep everything in the right place. I manually plunge the drill bit into my 0,0 spot before running the first operation to give myself an easy way to keep track of it.
For a two-sided board, consider putting a drill hole at your 0,0 and also at a symmetric location on the right edge of the board, so it’s in the same place when you flip the board over.
A good starting point for your cutting speed is 10 inches/min. And you shouldn’t need to cut deeper than ~.015" to get good clean traces. At that speed you should be able to do it in a single pass.