I have the APM 1 with the Mega2560... I can upload using the Mission Planner just fine. But I wanted to try the Arduino software, and tried to upload the Blinky program. I can't seem to get arduino to upload the software. avrdude just keeps timing out, and it appears that the program on the APM (uploaded from the mission planner) continues to run.
I've tried to press the reset button, and I've setup the COM port as specified. I've also read the manual, but no joy.
My APM1 acts the same way.
I had the same problem with two APM 1 2560 boards and it turned out to be a bad FTDI cable. I was using a new FTDI cable purchased from 3DR and nothing would load consistently from the Arduino IDE. So I purchased a different FTDI adapter from OSEPP in Washington State (http://osepp.com/products/breakout-board/osepp-ftdi-breakout-board/) and everything then worked fine from then on. 3DR did replace the bad FTDI cable, but I have not checked out the new cable.
Hope this helps,
Go to MP, than upload HIL mode.
Than use arduino to upload whatever you want. It helped for me. Might be it was a random thing, but i just did it this way.
Hope it helps.