I am not a professional luthier -- they will probably tell you not put on any markings
For little children, I put coloured pieces of tape: Now put your finger on the Green, now the Blue! See how that sounds like the 'Blues'?
Ok, here we go: Green, Blue, Red, rest, green, blue, red, rest, and again...
Some EUBs put markings by drilling 90 degree into the fingerboard between the E and A (bottom two) strings, filled with a metal or a plastic rod. NS design has a nice look, imho. People coming from the fretted world like them. I don't.
I think the left hand and your ear are connected. Intonation is determined by the key you are playing. Try it out for yourself: Take a pencil, and mark on your fingerboard where F# sounds perfect in the key of G major. Next you play the E minor scale, and you mark where G flat sounds nice and sad. Mark the spot. What is going on? The two pencil marks are not the same! Yet it is the same note on the well tempered piano! You tell me which one you are going to mark permanently on your beautiful ebony plank?
Here is a better idea: Why don't you mark the back of your neck with various tactile Braille markers for various positions? Surely that might be more useful, just like the Eb or D necks have their use.