The MikroKopter tool, or short "KopterTool", is a free available program. With this program you can adjust and check your copter or even plan a waypoint flight.
A manual how to use the KopterTool you can find here:
The software of the different components (FlightCtrl etc.) is also available to other developers.
It is located in a Subversion-Repository. The access to it is described here: MikroKopterRepository
For that reason that AVR-Microcontroller are used by Atmel you need to have a so called AVR-Toolchain for Linux and OSX, or WinAVR for Windows.
Linux-User can get this package i.e. with the following terminal-command: apt-get install gcc-avr avr-libc. For Mac OS X there is an installer available: Crosspack].
You translate the sources simply with "make" and you will get .hex-files which can be transferred to the device via the KopterTool.
More detailed informationen you can find currently here: FlightCtrl-Software