You can use whatever you like to put your design on the guitar. You could draw it on with marker pen, paint it on, ink it, pencil it on, stencil it on, spray paint it on, use glue and glitter, you could use your own feces if you really wanted to.

It's like anything else; mkae sure the surface underneath is prepare properly first (i.e. that it's clean and if what you're painting on is going to be very thick, you may have to sand down the original finish, or at least the top clear coat), do your design, then you will need to clear coat over the top of it if you want the design to last any reasonable length of time. The main problem is making sure the clear coat you use to seal it all in is the same type of finish as the guitar originally had. For example, if the guitar is at first finished with a nitro-based finish, you can't go spraying a poly finish on top of that. You'll either need to match the original finish, or you'll need to strip the original finish entirely before starting.
Yes, I know everything. No, I can't play worth a damn.
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a good option is to light sand it just to remove the clear coats and draw whatever u like. Then just give enough clear coats so the guitars seems smooth and the paint doesnt feel like it's above everything else.
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and im not gonna paint the whole guitar... just maybe 1/3 of it.
Go Ibanez!