The Fretlight's fretboard is on average about 4 mm thick. To safely clear the lower PCM board you will want to leave at least 1 mm of space above it so you should use the same 1 mm spacing from the top of the fretboard. As such, recommend using a marker that is at maximum 2 mm wide and 2 mm thick. This size of marker will give you the safety of having at least 1 mm of clearance on the top and bottom of the fretboard and will not risk drilling too deep into the side of the fretboard.
Use a 5/64 drill bit to make the holes. Wrapped electrical tape around the drill bit at 2 mm back from the tip of the drill bit to block it from going too deep. Drill the necessary holes, insert the markers with super glue and use a very light sandpaper to even out the marker with the fretboard surface.