There’s lots of info here on workholding and positioning, lots of different approaches for different jobs and materials
Check out the e-book
Lots of people drill their spoilboard in a grid pattern and put the M6 threaded inserts in for workholding;
What I’ve found very useful is having the Shapeoko drill a grid of 10.1mm holes which I then stick small pieces of 10mm Aluminium rod in so that I can line up stock and parts vertical or horizontal with the machine really quickly and easily by sticking pins in the nearest holes. Make sure you tram and square your machine before doing the pin-grid though…