What are you using for an audio interface? The Music Man bass should NOT overpower the preamp of the audio interface if you want a clean sound. (this is before Logic is even in the picture)
Because the Ray has an active circuit, you aren't going to sacrifice tone or frequency response by running the bass lower. The might want to look up "gain staging" on the Internet.
As far as Logic is concerned, after you get the bass working well with the audio interface, then adjust Logic's effects. It all depends on what audio interface you're using and how you're monitoring the Bass's input level.
My first thought is the Stingray shound not be running full or near full volume... to much output will muddy things up.