Which tools best for which tasks and project workflow planning?

I am just getting comfortable with the basics of several CS tools and often need to use more than one to build a final product. Since I don't have a long history with the tools I still struggle learning which tool to use for specific tasks and then how best to use the variety of created assets in the various programs.
Currently using CS4 After Effects, Flash, and Photoshop to create web flash swf files. Most books, forums, tutorials, etc. focus on a given tool and how to use its features. I have looked but not found books that take you through a project start to end that spans several tools and using the best parts of each to accomplish pieces of the finished project.
Also, I find getting assets from one tool to the next does not always work out so well. For example, a text layer in AE can be exported a couple ways but by the time it gets into Flash it no longer retains the original text layer and is either rasterized or broekn up. So that is where better understanding workflow, if that is the right term, might help me ensure I use the right tool at the right time in the right order to minimize these kinds of problems.

The guys from Waterloo labs did something similar: http://goo.gl/JkOy
They used a sbRIO, which is very similar to myRIO and you should have no problem doing this with myRIO.  More info on their setup can be found here: http://www.ni.com/white-paper/11966/en/.  You may even be able to re-use some of their code.
-Sam K
LabVIEW Hacker
Join / Follow the LabVIEW Hacker Group on google+

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