How would I paint letters onto my bass if I wabt to keep the black paint job it already have underneath?
You could either

A: Paint them on
B: Paint them on then clear coat it (and have a little uneven spot that will prolly drive you nuts)
or C: Paint them on and clear coat the entire guitar.

I'd do C, but it may not turn out as glossy or good as you want...
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light sanding to get the clear coat off and then paint and add a new clear

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And have you figured out yet -

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It's you
Yeah, if you sand the entire body be careful to only take off the clear coat.
But then how would I seperate the letters? Like using cardboard and then cutting out what I want to write or using tape or what?
Cover the area with 3M BLUE Painters tape, thin as possible or use Friskett Masking Film.

Use whatever to mark out the letters, cut the film with an Exacto knife or razor blade.

The film is very thin so you need no pressure, so you don't damage the paint..

Sand and seal/prime.

Paint it.

Clear it.

You should probably do it properly, than not, but that is the basic way of doing it.

Really, you need an intercoat, sand that, then lacquer etc.