Simplify 3D allows specific settings for the "bottom layer". However this really only applies for the very first layer printed on the bed - not necessarily the model's first layer. So far I have not been able to apply "bottom layer" settings (speed, height, width etc) in order to guarantee a very clean and accurate first model layer when I print on top of a raft. All "first layer" settings are applied to raft layer 1, not model layer 1. Obviously it may be critical to control the raft's first layer in order to guarantee good adhesion, however it can be equally vital to get the model's first layer perfect as well.
In addition, the same principal applies for other downward facing horizontal model surfaces (those printed on top of a flat support layer). These may also be highly visible layers since part orientation is often determined by printing behavior, not the model's real-world orientation. This is of great importance for those like us, who are printing mechanical parts which often have several overhanging flat surfaces which will be highly visible in the final model. Unfortunately Simplify 3D does not differentiate these layers at all and they are printed at high speed - often resulting in a rather awful appearance. Yet the bottom of the very first layer - often the bottom of the throw-away raft - is beautiful ... because it could be controlled.
I suggest that downward facing horizontal faces be given a seperate definition, and that these "down-faces" be allowed to have at least a slower speed override (preferably also width/height). This would make it SO much easier to create great looking models built on rafts and with support material so we can have complex mechanical models with numerous overhangs - something that has been the domain of only the highest-end printers.