Can't help you much with Simplify3D. Also dont think you can ad a brim with MPrint (only a purge wall which is a bit of a waste of filament but good for letting layers cool).
As for your roof having holes, in MPrint, if you go into "create profile" and edit the C code, you can increase the roof thickness, thus getting rid of those holes on the top. There's alot of options when editing the C code, and It'd be possible with months of testing to really push the limits of the printer. (also I recommend for MPrint always printing on "High" quality" and changing your layer height, infill etc to suit).
As for brims, I use Solidworks, and sometimes i'll design my own support. Also if im printing a small print, and want a pause between layers to let it cool (so it doesnt warp), ill insert a thin "wall" roughly the same height as the object on the opposite end of the print bed.
Just a couple tips.