You need to configure, compile and upload a whole new firmware. I assume you got Sprinter preloaded on your electronics and will need to start from the beginning.
Go to Sanguino.cc/useit and follow the instructions for your OS. Use an older version of the Arduino environment, 1.0 has issues but 23 works.
Download a copy of the Sprinter source, or other firmware if you like.
Unpack the source somewhere and open the .pde file in the Arduino environment.
Open configuration.h and work your way through the file making changes to suit your machine. The defaults should suit a standard Prusa for the most part. If it makes no sense at all to you, look for a beginners C tutorial, but the file is pretty self explanatory. Hopefully your thermistor is one of the common types and you can just define the thermistor variables appropriately, if not you will need to generate a new table and include it in thermistortables.h. I'm not quite sure how to do that, but the program that generates the tables is written in python so start by installing that.
When the firmware is configured, select Sanguino from the tools->boards menu, select the com port, hit the upload button.