I meant to touch on this awhile back, but there is a helpful AS3 feature buried in the ActionScript publish settings called "Automatically declare stage instances". By Default it is always set to true. I have found that when I am designing in the Flash IDE and scripting in Flex3 that I am better off without this feature enabled.
Basically the Auto Declare feature means that any movieclip on the stage will automatically be declared in the class containing the movieclip. For example, if you place a movieclip of a circle on the stage and give it an instance name of "ball" then the document class will automatically declare a variable called ball similar to you typing in "public var ball:MovieClip;".
The problem with this (at least in my development setup) is that I can not make references to the ball variable in Flex since it does not get declared until runtime. If I try to help Flex by declaring a new variable called ball I will get a duplicate variable exception when the code compiles. I could always cheat and make a variable with a different name such as "ball_mc" and then target the movieclip by writing the following: var ball_mc:MovieClip = this["ball"]; It works, but now you have 2 references for every movieclip and it also looks pretty hacktastic.
To get around this problem, go into the action script settings and turn off the Automatically Declare Stage Instances. In Flex at the top of your document class declare the following variable: public var ball:MovieClip; It is very important to declare all movieclips that are in your Flash IDE as public, otherwise you will get an exception when it tries to compile. By following this setup, you will now have 1 reference to the ball movieclip and you do not need to do any hacktastic tricks to gain access to it. The only hassle I see is trying to maintain the instance in two places, but I don't see any way around that until Flex and Flash are integrated.