What's the best way to mark wallboard for electrical box openings?
You have to measure really accurately with this. With drywall you might be able to go with a rough location and cut the edges while the board is held or lightly screwed into the wall, but that probably won't work with something as rigid as plywood.

The opening in the wallboard should be sized to the electrical box. Then the cover plate helps you hide any gaps. One handyman tip is that they sell extra-large cover plates to help hide sloppier cuts!

You can also buy tools designed to help mark these cuts:
https://www.amazon.com/Calculated-Industries-8105-Drywall-Electrical/dp/B00YX8KZGO/
or
https://www.amazon.com/HandyMark-Drywall-Marker-2-Pack-HM1002-BF/dp/B000V5MPZM/

One last idea if your cuts are significantly off is to replace the electrical boxes. You can get old-work boxes that attach to the wallboard (rather than structure). Just trace the outline of the box onto the wallboard and cut. I like to use an oscillating saw for this.