The way I have done mine is to put a copper plug (pad) into the grub screw hole. I have done this by using a bit of solid core earth wire from twin&earth cable just lightly swash it with a hammer and then cut a piece off that will fit down the hole so that the flat bit is on the shaft then just tighten the grub screws. That way you don't mark the shaft.
I have found that it is not necessary to put a flat on the motor shaft. ..Clive