Hi,
I would start by looking at how people are integrating code written in C and C++ into libraries:
Arduino Playground - Library Tutorial
Alexander knows LOTS more than I about this ....
...but those libraries have code that gets linked by the AVR stuff inside the Arduino IDE setup...
Also another Library tutorial:
http://www.arduino.cc/en/Hacking/LibraryTutorial
Regards, Terry King ...Not Yet Pro