Thw WT800 is not a stereo head. It only has two power amps to power multiple cabs or bi-amp. In order to treat your signal as stereo, you would need a separate preamp. With a separate preamp, it looks like you could use the FX loop returns to feed separate signals to the two sides of the power amp.
To be more specific, you would feed one pickup directly into the WT800. Connect the FX loop send to the FX loop L return. Feed the other pickup to some external preamp (Bass POD XT, Sansamp, F-1X) and then connect the output of that preamp to the FX loop R return. The result should be what you're looking for.
The down side here is that adjusting your pickup balance will affect how much sound is coming out of each side, not just the character of it. This kind of stereo isn't really for putting a cab on either side of the stage, but rather for having individual control of each pickup's tone shaping from start to finish.
Here's another thought. If you want the appearance of stereo sound rather than the ability to manage each pickup individually, then you can again use the FX loop. With the tasteful use of stereo effects (chorus, delay, etc.), you can create a setup that will give you imaging options if you locate a cab on either side of the stage.
Good luck!
-bob