The hardware acceleration mode is set via an HTML parameter so it does not matter if you do not use the Flash IDE to compile the SWF.
When you publish your SWF file, the HTML file that embeds it contains
a wmode HTML parameter. Choosing Level 1 or Level 2 hardware
acceleration sets the wmode HTML parameter to "direct" or "gpu"
respectively. Turning on hardware acceleration overrides the Window
Mode setting you may have chosen in the HTML tab of the Publish
Settings dialog box, because it is also stored in the wmode parameter
in the HTML file.
Source: http://help.adobe.com/en_US/Flash/10.0_UsingFlash/WSd60f23110762d6b883b18f10cb1fe1af6-7bcea.html
Also, you may find this interesting regarding the Hardware Acceleration settings:
http://blog.kaourantin.net/?p=74