You can change the version that your SWF publishes in by going to File->Publish Settings (keyboard shortcut Ctrl+Shift+F12 PC, Option+Shift+F12 Mac). Make sure that Flash (swf) is selected on your Formats tab, and then click on the Flash tab.
The first field available on the Flash tab will be a dropdown labeled Version. Click on that to expand it; it should list all available versions. Select the version that you want to publish in, and then click OK to make sure the changes "take" and are saved. And that's it; you're done. Your SWFs for this file will now publish in the version selected.