Both the AIR SDK & Compiler and the Flex SDK may be used for pure AS3 development, and FlashDevelop supports both of them. So it's really up to you if you want the all-in-one AIR SDK & Compiler, or if you want to stick with the original Flex SDK and manually overlay new versions of AIR from time to time. Personally, I find it easier to download one thing that just works after unzipping, so I go with the AIR SDK & Compiler. I know that others have always used the Flex SDK and they don't see a need to switch. Both choices are fine.
I don't use FlashDevelop personally, so I don't recall where the SDK gets set for your project, but when you find it, it'll probably be pretty obvious from the SDK's name which one you currently have.