Here's a collection of material that should help:
Here are a few specific snippets from that collection that apply to your specific situation:
-To reduce color differences when comparing colors in Catalyst and Illustrator/Photoshop, set Proof Colors to "Monitor RGB" (In Illustrator, go to View> Proof Setup and choose Monitor RGB). (From Ian Giblin's slide deck, pg. 19)
-When creating documents in Illustrator that will be imported into Catalyst, set the document color space to RGB. There is a new document profile for Flash Catalyst built into Illustrator (select it from the New Document menu in Illustrator's new document dialog box). This does other helpful things like turning on "Align to Pixel Grid, and setting your document size to the commonly-used 800 x 600 pixels.)
-Regarding the choppy logos, try using the "Optimize vector graphics" command in Catalyst (select your logo on the artboard, and in the Heads-Up-Display, choose Optimize artwork and then Optimize vector graphics. This feature is made for optimizing vector art for good performance, while still maintaining the ability to edit the vectors later if needed. You can also convert the logos to raster images right inside of Catalyst, by choosing "Rasterize" instead of Optimize vector graphics. More details are in this great FlashCats blog post.
Thanks so much for all that!