You may want to ask somweone else but from what I can remeber... You shouldn't use the JB3s on-board gain... I haven't heard too many good things or experiences from those that have... From what I understand, it can cause all kinds of issues and different types of distortion... Not sure though cause I've never done it myself.
When ever I run my JB3, I always run it flat(neither increase or decrease the gain)... I've never run too hot... My levels are usually a little low as I am still running w/o a pre, but I have had great results normalizing my vollume in post production (wave editing software)... I plan to pick a pre shortly and not to mention all my taping has been bar-shows, however, I've yet to have any issues... I've been loving the pulls to date... I can see myself runnning into issues at larger or outdoor shows w/o a pre...
One thing for sure, if you're not going to run a pre, you'll definitely need to run some line matching transformers... It's a cheap fix that adds about +5 gain until you take the plunge and shell-out for a pre