It is a good idea to change the neck- and fretboard markings on the M3 so that they support the logic of its tuning. If you don't, you will almost certainly be thoroughly distracted by the familiar markings in 3rd, 5th, 7th, and 10th fret. The markings are extremely important as a reference for 'offline' analysis, and I encourage you to take their visual appearance very seriously.

If you start to modify the standard markings, you will find, surprisingly perhaps, that when you play you orientate yourself almost exclusively by using the small marks on the side of the neck. You can add your own by drawing a new set of symbols on a thin piece of tape attached to cover the factory made dots. What you put on the fretboard itself does not serve any functional purpose, it is purely cosmetic. If you ask your guitar doctor to make permanent changes to either the dots on the side of the neck or the inlays on the fretboard, you are likely to see a hefty bill at the end of it so think carefully about such a modification before you order your personalized, cool-looking, M3 axe.

Since patterns on the neck repeat every four frets I suggest you use markings that symbolise the numbers 0, 1, 2, and 3. Thus, you would use the same markings in frets 1, 5, 9...; the same markings in frets 2, 6, 10...; and the same markings in frets 3, 7, 11... You can leave the frets 4, 8, 12... blank. My choices are a small dot for 1, a square cut in two for 2, and a long dot for 3. You might want to try something different, it is great fun to experiment with.