The global mapping is only meant to be used to hardwire a specific action to a button. If you don't want that but instead want to benefit from the diversification offered by Behaviours, leaving the global mapping table at its defaults is the best thing to do.

Then, regarding control of Flash:

1) If you're running your Flash app inside a browser: 
Change the mapping of the respective browser under Prefs > Mapping > [Name of Browser].

2) If you're running your Flash app as part of a native Mac app of your own: 
Make use of the Behaviour Construction Kit to create a Behaviour for that Mac app. Find a video tutorial on the BCK here: 
http://www.iospirit.com/products/remotebuddy/videos/#behaviourconstructionkitintro

Hope that helps.

Best regards, 
Felix Schwarz