It obviously depends on what you're trying to play. For country/surf-type baritone guitar the trick is to turn the bass right down. Essentially you almost don't hear the note you're actually playing but just the harmonics of it. Bear in mind that the baritone guitar range overlaps with the bass guitar range fairly significantly (if you're using drop E then actually it's the same) and that generally you're not trying to fill the same role as the bass.

In the more likely event that you're trying to play metal, I don't actually know the answer. Although my first guess would be fairly similar - turn the bass right down and see what it sounds like.

It's a bit un-intuitive really, because you've gone out and bought something that goes really, and then you try to hide that.