RBW, there is a 'learning curve' that we all went through when we got our first Alembics. The pickups and electronics are extremely neutral and powerful. I clearly remember at first thinking, 'is this all there is?'.
They are incredibly clear: Think of the difference in big-dollar recording studio monitors versus first-rate home stereo speakers. The studio monitors are unforgiving in that every sound is reproduced so very accurately they lack what we perceive as warmth in home stereo speakers. This is where you're at with Alembic pickups and their tone circuits.
As Micah always reminds, your instrument is the bass + amp/speakers + any effects. This signal chain is your instrument. A bass in a case is silent, as is an amp with nothing plugged in. And as with any bass, the amp it's plugged into makes all the difference, and your usual settings for your other basses may not be best for the Alembic.
When I got my first one, my amp settings went out the window. The pickups were the first I owned where I could easily and clearly hear the difference in one brand of string to the next. I'd owned lots of great axes, but I never heard the difference in strings until I got an Alembic. Spooky.
Settle on the strings (Rotos, it sounds like), work with Q controls, and find the amp settings to suit. It takes a little while to wrap your head around all this, but there is nothing, and I mean nothing like an Alembic, nor the people that build and support them, the best people in the instrument business I ever dealt with by a mile.
PS When I wanted that Squire / Entwistle 'clavinet on steroids' tone, I'd use the neck pickup with the Q almost wide open and use a pick back around the bridge pickup. Sounded like ice picks . . . . . .