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I'd start by realizing that generated code is not normally going to be appropriate for production, and plan on rewriting it. Failing that, here are a few strategies that may work for you:
You could use a Presentation Model to encapsulate the business logic, and then operate that PM from the View that Catalyst built for you http://blogs.adobe.com/paulw/archives/2007/10/presentation_pa_3.html
If you use Robotlegs (or you'd like to), you can approach it from the other side, creating a Mediator that can operate your View based on events it receives from the rest of your app.
In such an example it would be difficult to go and re-write the whole code base, I assume this is what Flash builder is for. To build the presentation layer. I see how they built the buisness logic which is what I thought it would be like.
Do you have any other tips for a project that uses flash cat to build the presentation layer and fb 4.5 to build the business logic?
It's actually much easier to deconstruct and rewrite even bad code than to start from a blank slate. But, if you actually read what I said, I gave you two other options. Pick one
I find the workflow easier to start with the component logic in Flex, than use catalyst to build the skin and supply the graphic assets as a "theme", rather than use it to build a fully working application. I will usually mockup the app in catalyst first, build the components in Flex, and finally polish up the final graphics in catalyst.