So I am trying to import designs from AI files. I know that I can't just open them in flash and that I need to either, copy and paste the design from illustrator into an Action Script 3.0 file. The issue is that the elements get all messed up and it doesn't always copy it with the layers correctly and it ends up being a mess. The other way is to export the ai to a swf, then import it in flash but this has the same issue.
How can I import designs from illustrator and retain the full design composition without having to realign and fix everything in flash?
Without seeing what you are doing, its difficult to describe how you might fix the problem. I usually import the .ai file into Flash. When you import an .ai file, you can select the layers to be imported and you can set the resolution of the imported files. You can select to set each ai layer as a flash layer, or to put each ai layer into a new keyframe.
Most of the time your illustrator artwork will import correctly into Flash. There are some exceptions in very complex artwork or gradations. If you are preparing art in illustrator to be used in Flash, then be sure to start in illustrator with a file set for the web. You don't want to do a lot of precise work in illustrator at 300 dpi and then have it import into Flash at 72 dpi. Start with the resolution that you need to end up with.