LeftyBassist.com

I have two maple fb, righty necks, a JB and a Strat. In the past, I've used decals, even a sharpie, but they all rub off. I want to do this right and have the tools to do it with, including a drill guide and a manual drill about the size of a pen. I will do the work carefully carefully. Fortunately, there are YouTube vids, but I figured that some of you might have done the job before. Maybe you have tips or cautions?

Both are finished necks. Fender dots look like decals that are covered over. What materials have you used for the markers? Did you use some kind of clear coat over the dots when you've got the dots in? I'm using a 1/16 bit after having seen a vid. Is this the size you'd use? Bigger?

I've used clear nail polish with success!

When in doubt, nail polish will do the job. I've used tinted ones to cover mars on instruments. The clear stuff ought to do what I need.

I've used a small drill - about 2mm in a handheld pinvise. Just lay some masking tape on long the edge of the board and mark positions. Do the double dot 12th fret first so you don't get carried away and put one dot by mistake. Just drill in enough to make a dimple.
Get black paint (I used exterior metalwork gloss from a thrift store) and after making sure it's well mixed, use a wooden cocktail stick to drop a blob of paint into the dimple. Wait until it's dried then smooth off the ridge around the dimple the drill would have made (and that stopped the paint running outside the dot).

You can make your own side dots, very easily. Go to the hobby shop- and get some small diameter plastic rod. Say, 1/16"
The side dot material I buy for my builds is cheap, and easy to use. TAPE OFF below the fingerboard edge. Measure the exact spot you want to place them... and use a very pointy tool- I use an Awl, to make a guide mark for the drill bit to fit in. Drill small holes that are close to or slightly undersized - by say a few thousandths, and cut a small piece of the rod, run it against some 320 sandpaper to make it slightly conical in shape, then- put a SMALL drop of gap filling super glue in the hole, and tap it into the hole you drilled using a small hammer. Trim it NEARLY flush, if you cut it, use end nippers and a feeler gauge to make sure you don't rip the plastic to a level below the surface. Sand flush with a block and 320, then 400- and some oil, or touch up lacquer. If you're doing just the edge of the board, this works great.
If you are inlaying the dots to be half- on the board, and half on the neck- its the same procedure, but with more care not to really mess up the neck finish.

Fender uses plastic dowel material and finishes over it.
Stew Mac sells plastic side dot material. It’s super cheap and it’s just tiny plastic dowels. Drill to desired depth (you don’t need much at all), insert dowel then trim. I did that on my Höfner Cavern and a couple older Hoffies that didn’t have side dots at all. Then I touched up the nitro over the dots once I had them flush.