I set my GT1000- everything runs through the same amp modeler, the same virtual EQ, then, I just assign the knobs with on-the-fly EQ depending on the bass.
No issues- the main thing to look out for is guitar OUTPUT, I set the output signal based on my least hot bass- say my Passive Reverend, so at max volume, output is ideal, for my hotter actives, I just roll the volume down.
Some multi-effects like my Boss are output sensitive, if you aren't careful, you'll clip the output so everything is really harsh especially when it's emulating a tube amp- or the inverse, it'll sound weak and boring.
Think of it as gain.