Is 1280 board compatible with Arducopter 2.6 or i should go with 2560?
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It's compatible, but you're not going to like turning off functions to get it to fit. Take the easy route and get a 2560.
The biggest issue with the code fitting on lesser than current boards at the moment is the inclusion of all available GPS drivers in the default AC2 build in order to accommodate the auto-GPS detection. If you take a look at my previous posts you'll get an idea of what's involved. The main thing is that you won't be using Mission Planner to load code- you're forced to edit code and compile/upload via a development utility.
is it just for 2.6? i mean which version can i use with mission planner?
Seriously you want the latest code. Don't run old code just to use a 1280, if you have the opportunity to get a 2560 instead.
i am building a 99 cm y6 and i read too much disappointed review of pid setting. Cause i am not good at it (i dont want to ruin all the efforts and money before you fly just in the tunings). i took of my apm from bixler to use. But cant be sure to all the pid tuning. I have KK's in my quad and Tri love the pid free.