So as a totally newbie, I see so many choices that it's a bit overwhelming... If I understand the major configurations/history correctly..
APM 1.X based on ATMega1280
APM 2.x is an ATMEGA2560 and ATMEGA32U-2 (for USB) based platform
ArduPilot Mega (APM) 2.6 running Arducopter 3.0.1...