I'm using Simplify3D 3.0.0 and a MakerGear M2 with a dual extruder head. T0 is the left extruder and the one I consider the "primary" extruder. T1 is the right extruder. T1 is offset from T0 on the X axis by +31.1mm.
I have set up my printer with PLA on the left side and PVA on the right. I notice that you have a process setting that comes with Simplify3D 3.0.0 that is for "PLA (right), PVA (left)". I took this process setting and modified it trivially so that PLA was on the left and PVA on the right. It shouldn't much matter because they have very similar properties; it's just a matter of which one prints the object that is meant to be the printed part, and which one prints the object that is meant to be the support.
I found one fairly major issue with the dual extruder printing. Because there was a lot of confusion figuring out just what it was that was going wrong, I have edited my initial response, removed several follow-up posts, and condensed it to just the single issue that it boiled down to.
On startup, after purging, the left extruder goes to the starting print position and begins without the inactive extruder being retracted. The gcode shows that the gcode inserted for tool changes does not do a retraction on either tool until the 2nd time that tool is made active. Unfortunately, that means that the inactive tool, having just been purged but not retracted, will ooze all over the first layer of the print. The solution would be to always first activate the tool that is not the first to print, retract it, then activate the tool that starts the printing; and then do the retract/restart for every tool change after that.