The newest Slic3r has a feature called Modifier Meshes. It basically takes Simplify3D processes one step further. You can import another STL and lay it over your main model and then define slicing overrides where the two models intersect. So with Simplify3D processes you can change printing parameters as you move up the layers. With Slic3r's modifier meshes, you can change printing parameters for any part of your model, in any orientation. I really hope something similar comes to S3D.
I also want to say that I find Slic3r's implementation of this, the idea of having a common base of slicing parameters and then overriding specific settings, to be a bit cleaner. In S3D, if you have say four processes in a setup and then decide you want to change one common setting, you have to change it four times. So also consider implementing a method of 'locking' settings between processes and then just overriding the ones you want to change.