Both work well with the Simple. In Simplify3D you simply select the Printrbot Jr in the pulldown for the process and set the bed size accordingly. Simplyfy3D's capabilities are hard to beat with manual supports, temp per layer, the very best visualizations, auto speed setting per layer. You get what you pay for.'
but... for FREE you can use Mattercontrol written by the guy that wrote the code in Marlin for auto leveling in the Z-Axis. Mattercontrol will allow you to use auto leveling without the proximity sensor. It uses Slicer, and a ported version of Cura.