Steve,
The filter system can take a little getting used to. Here's my opinion (others will likely chime in soon).
Start with the bass and treble switches flat (middle position). Set the pan knob to the center detent, turn the filter knob all the way open and flick on the Q switch. If you're not sure which way is on, hit an open G and let it ring out- while that G is happening, quickly turn the filter knob back and forth. You'll hear a pretty distinctive 'wah-wah' sound. Flick the Q off and try it again..... hear the difference? Once you've spent a few minutes playing with you new Wah pedal

flick that Q back on and leave it there while you start experimenting with the pan.
With the Q on and the filter wide open you should get a VERY bright and distinctive Alembic tone. From there you can start playing with the pan to add a bit more beef (by favoring the neck PU) or roll the pan towards the bridge to get some more bite/cut though. At this point- are you hearing the difference between the neck and bridge pickups? Once you're comfortable hearing how that pan affects the sound you can find your own 'sweet spot' with the pan. Once you're happy there, start rolling back the filter in tiny increments and listen to how a tiny turn greatly affects how your bass sounds in that spot you've chosen with your pan. It took me at least a couple hours to really start to come to grips with my first filter equipped bass- keep experimenting and I promise you'll get to a point where you like it.
My bass is signature equipped, but I tend to play with the pan set to roughly 60/40 (favoring the bridge) and I usually play with the filter at about 2/3-3/4 open. I like to leave the Q switch off for fingerstyle.
Check the FAQ section for info on how to adjust output with the trim pots and/or advice on raising/lowering the PU's. I've never touched mine, so I can't offer any real advice.
Toby