As Andy said, standard practice is to paint up to the neck/fretboard join line on necks with a rosewood or ebony.

Where Andy says he then waxes the side of the fretboard, most manufacturers will clear-coat the neck and sides of the fretboard, whilst masking off the top of the fretboard. Sanding down the clear-coat should then get rid of any join-line ridge. This also helps seal-in the fret ends.

There is no right or wrong way here, just personal choice.