There should be a link in the RAMPS 1.4 section of the RepRap Wiki for some test code you can load onto your Mega2560. This is a simple script to flicker some LEDs so you know the boards powered correctly as well as moving your motors back and forth so you know they are connected and working.
For the firmware, I think Marlin is the default for Prusa's, though Repieter 0.91 should work as well. The nice thing for a beginner is that Repieter F/W has a configuration dialog to set a lot of the values in your Config.h file, so you won't have to browse thru a lot of code immediately. Eventually you will want to figure out what the different flags in the code do however.
For the software to connect to and controlling you printer, I would start with Repieter Host, though I have yet to play with the current release. You do not need to use the Repieter firmware, the software will work with Marlin. The firmware also should come with slicing software for converting STL files (downloaded from Thingiverse or Youmagine) into g-code that can be processed by the printer firmware.
However, I would check with / email the provider of your kit. They should have recommendations or links to guides for installing software and calibrating your prints. Google is also a decent choice for getting started.