Okay this might be a dumb question:
When using an outboard mic preamp such as the WA12, I would still be running the signal through the mic preamps that are built into my Apogee Duet 2. Is that correct? So the signal goes through 2 preamps?
Overlooked that question completely, until this moment.
Here's the short answer:
Yes!
(read on if you need more specific information and you are ready to consume a wall of text)
That is giving you actually set them right though.
I actually end up kind of using several amps and pre amps in my signal path when recording:
The EHX Black Finger compressor first in my chain, right after my bass, have a build in tube preamp that drives the actual optical compressor, then comes the Zoom B3 on which I run a bass preamp emulator into a bass amp and cab emulator, finally before my sound interface I run it into a tube mic preamp, also there's a preamp build into my sound interface that my signal run through before it is converted and send to my computer.
As if that weren't enough, when recorded I often copy the recorded track into 2 tracks, and beside the other VST's I usually place respectively a bass amp emulator and a guitar emulator last in the chain of the respective tracks.
So my usual recording/mixing approach actually makes my bass signal run through quite a few pre amps and amps before I have the final result.
As said it will cause no problems as long as you set the different amps and preamps so that you make sure they will sound good together.
I also know several people who actually stack preamps live and feet it into their amp, which will also have a preamp stage, to get their desired tone.
Hell I do it myself.
With my live and band rehearsal rig I first run my bass signal through my Black Finger, which as mentioned actually has a build in tube preamp, then into my solid state Trace Elliot combo's input, which means preamp stage, the signal from the preamp of my Trace Elliot amp is then fed, via the combo's tuner output, to a Joyo Orange Juice, which is a small analog Orange Amp emulator, which again means it actually acts like one more additional preamp, and then finally into my Bass King tube amp's input, so basically into my tube amp's preamp stage.
Further more my signal chain contains a Joyo California sound, which like the Orange Juice is an amp simulator, acting like a preamp, in this case I stack it with my fuzz and use it as a tone control for it, and then I also got another Orange Juice pedal, which takes care of my overdrive tone.
So that was the long answer, it is absolutely possible to run your bass signal through several preamps and with good results, if only you are aware that you will need to adjust the individual preamps so that they'll actually work together, instead of against each other, and listen carefully.
No problem!