The internal trim pots are for each preamp's gain. If you've got one (like the Essence), it controls the overall output of the bass.
If you've got 2 (like a Signature Deluxe) then you get to control the gain of each pickup separately. This is cool because you can now set the pickup height without regard to output. Normally, the bridge pickup is pretty high and the neck pickup is pretty low. If you prefer the sound of the neck pickup higher, you can raise the pickup, then balance the gain with the other pickup by comparing the volume at the extremes of the pan control, and then adjusting the trim pot (in this case, turning the neck pickup trimpot down since the closer the pickup is to the string, the louder it is).
It's a little harder with 2 trim pots to adjust the overall output because you have to adjust 2 controls. Just check the pan control before you close up the backplate and make any other fine tuning adjustments once you've got the overall output to where you want it.