Well your picked the right software! We collaborated a lot with MakerGear, so the settings that the software comes stock with are actually already the state-of-the-art best settings we are using with our M2's. You should literally be able to load a part, slice, and print it without any extra configuration.
As far as the typical process for 3D printing, it's a little more complicated than traditional 2D printing, but not by much. Just drag and drop an STL or OBJ model onto the virtual table to import it. Use the mouse and keyboard shortcuts to get the part positioned appropriately (see here: http://www.simplify3d.com/support/#FAQs
for the shortcuts). Next, add a new FFF process which should allow you to change all your typical slicing settings. Then you're left with what we call the three P's of 3D printing; just prepare, preview, and print! Press the prepare button to create the actual G-Code instructions. It should automatically ask you if you want to preview those instructions once it's done. You can use the sliders at the bottom of the window to move through the preview and see what your 3D printer will be doing. And finally, you should already know how to print! Just press Ctrl-P (or Command-P on a Mac) to bring up the Machine Control Panel. That's what you use to manually control your machine or start prints on it. Make sure to plug in your M2 and select the right port to connect. Then just press the Run button and select your G-Code file to start printing.
That's the basics! We're still working on putting together some quick tutorials to walk you though the process, but that should be enough for you to get going. Glad your liking it so far!