By using the -d commandline option and ifdef and endif in the WDL script. Actually my own freeware tool, GS-Startup Manager, already does this, as well as providing a setup panel allowing the user to choose resolution, and a splash screen and loading bar for non-Pro owners. Version 2.0 will be out in a couple of weeks:

 -

The loading bar supports games packed with GST-Builder and Brain Editor (ie. it shows the progress of the unpacking process). I would be interesting in supporting your packer if you are interested.

Cheers,
Keith