create your app with no off-stage objects using 1024x600.
also create a main swf using an 800x480 stage that loads and resizes your app. likewise for 640x480.
Not sure from your post of you already tried this, but in CS5.5 you can resize the Stage in the Document Properties dialog box and select the new option to resize the contents of the stage. This feature was added specifically for the scenario you described, e.g. deployment to different screen sizes.
Take a look at:
- Scaling content on the Stage (Flash Help)
Video: Flash Professional CS5.5 - Scaling Assets (4:20, Adobe TV)
ActionScript 3.0 Example: Scaling and resizing assets for use on multiple screens (Paul Trani, cookbooks.adobe.com)
If the bitmap file size is your concern, you may want to try this.
File - Publish Settings, under Flash tab, reduce the JPEG Quality, and publish your content.
e.g you can reduce it to 30 to publish a small screen size version, 50 for middle screen size, and remain 80 for original large screen.
Good thing is you do not need to scale your content, or keep multiple copy of FLA source.