MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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Octoprint works well on my printer. It's basically universal to all printers so it's just a matter of settings.
As for uploading gcode, most 3d printers use a computer program such as Pronterface or Octoprint to send the gcode over a USB cable. For beginners I would recommend a software called Repetier Host. Octoprint also does this job well too, but requires much more setup. Cura is also user friendly, but kind of assumes that you have an LCD so it seems to be missing some features.
Dual extruders are not entirely feasible on ToyREP because of its low price point and limited motors. Not to mention that adding a second extruder takes at least 20mm of space off the Y axis. In my opinion, if you want a dual extruder setup you should save up and build a prusa i3.