For offline viewing I strongly recommend rendering out to QuickTime ( i go uncompressed) and using Sorenson Squeeze to output an FLV for Flash to use. You can import the FLVs into flash to use as MovieClips if you need to control them as graphic elements otherwise keeping the FLVs as external video files is recommended as it will keep the video loosely coupled with the swfs frame rate.
You can use Flash’s Media Encoder but Sorenson Squeeze ($150?) will give you better results because of it’s 2 pass encoding option. I have not tried to used the direct to swf/flv out of AE and don’t know the quality of output but that is a inherently less flexible workflow.