I was using ReplicatorG and it doesn't have separate extruder settings unless you're doing a dual printer file.
I installed MakerWare and had some luck getting it to use the left extruder (2) as the support material, however I was unable to get the ABS to adhere to the PVA. Eventually gave up.

Any ideas?

Oh and I did try Slicer, and after setting up all the different profiles (ie: left, right and dual) for the extruders, I tried again, and no matter what profile I select it won't heat up the left extruder nor the print bed.
Back to MakerWare.
(and yes I have it set to extruder=2)