I installed the Arduino-QP (1.5.x) yesterday and tried the build-in examples (e.g. blinky). It worked smoothly within the QM tool for UNO board. When I switched to Mega2560, I couldn't download the code. It appeared that arduiniodue.exe did not select the right programmer for the board. It used "arduion" for -p of avrdude.exe instead of the correct "wiring". I slightly modified the source arduiniodue.c to add an additional command line argument for programmer type. The programmer can now be defined in QM as an environment variable defined in Manage External Tools.
If I understand you correctly, if I download the latest version of QM, and set an environment variable, then it will now upload to a Mega2560. Yes? What is the environment variable?