I wouldn't worry about getting enough bass. I've had Dark Stars, Bartolini triple coil (kind of like a series setup in each pickup, with a dummy coil in the middle) and early Alembic trapezoidals, which are in there now.
My favs of this list are the Alembic and Barts. (The Dark Stars were a little wooly. I'm looking for an EB3 or EB0 in which to put them.) The Alembics are by far the clearest sounding, but are also probably the priciest. I don't know if the fact that my pickups are on the older side and have a very low impedance (resistance is well under 1k ohm) makes a difference in the sound. The newer ones may have a slightly different tone and the non-Series pickups may also sound different. However, I would not suggest the Fatboys. My only real complaint about my pickups is that they are microphonic and thus start squealing before I can get any really fun feedback out of the bass.
I'm also waiting on a pair of SGD ND3 pickups for my Modulus Q6. They get great reviews, although it takes forever for David to get them made and shipped.
Whatever pickups you use, they should all work fine with Alembic electronics.