I use Flex (not the framework, just the coding environment) to program all of my games and I will NOT go back. It has way too many benefits over using the Flash IDE. Yes there are a few things you have to deal with but the benefits outweigh the downfalls if you ask me.

I created a video about this if you want to learn from my mistakes and get started :P
http://cheezeworld.com/how-to-use-fl...only-projects/