Use these - you can get them at Staples. They're 1/4" diameter, stick on, and last for quite some time. I like to take a Sharpie and draw a nice black dot in the middle - it will not leak through. I use these on every bass I have that I can't see the position dots on, including a '66 Jazz. When they do finally come off there is practically no residue, and what there is can be rubbed off easily with your finger. It will not mar your bass in any way.
These were recommended to me by my tech of many years. His side gig is being one of the techs for the Fab Faux (look them up). It's what Will Lee uses on his gear. I've been using them for years now and short of installing LED's they're the best alternative I've found. No paint/white-out, no fuss, no muss.
Yam BB Club #3; Lane Poor Club #5;
Haggy Bass Club #7; Warmoth Club #18;
Tele Bass Club #24; MM Sterling Club #25;
B.C. Rich Club #52; U.S Peavey Club #306; Sunn Ownwers Club #82