The pad in the preamp input is a resistor that reduces the gain/sensitivity of one of the inputs. The reason you want lower gain is in the event that instrument you're plugging in has too high an output level for the regular input. The amp designer wants to design in enough gain so a low-output bass produces enough signal to drive the power amp to full output. If you have a lot of input gain AND a high output bass, you run the risk of overdriving the preamp.
So, the answer for you is to turn up the volume on your bass, turn the preamp gain up (if you have one) and see whether you get a clean sound. If you get distortion, then try the padded input and see if that sounds cleaner and that you can still drive your rig to full volume.
Alembics are all active, and generally there's a trimpot in the control cavity that lets you adjust the output level over a wide range. If you play multiple basses, you may find it easier to dial back the Alembic's output so it's closer to your other instruments.
Because of the active electronics of your Alembic, you can crank the output level up and down without affecting the tone (try turning down the output level on a passive bass and you'll lose treble).
There's an interesting psychoacoustic effect where everything sounds better when it's louder (just like your drummer always told you), so it never sounds good when you turn down the output level or used the padded input, but it really will sound better when you're not doing an A/B comparison.
David Fung