I use openscad which makes it real easy to spilt models into two parts.

You just comment out the bits you want in a different colour, render and save as stl and reverse for second part.

You then load both stl files - make sure they're not moved to the bed surface.

In s3d (actually really crap for dual extrusions at the moment) you need a seperate process for each model. Load the dual extruder profile and select left for one model and right for the other.
Personally - for dual extrusions - I'd use makerware - the nozzle wipe walls keep the print clean. It takes a lot longer - but you do get really nice prints.
I found with s3d that the edges of the model acted as the wipe and get crusty with both colours. Plus you'll get bits of plastic mixing in the body of the print as well. It's not good.
And ticking all the nozzle wipe options - makes absolutely no difference at all.

s3d have promised a lot of dual print improvements in the next update - so fingers crossed. :-)