I've got this. What you need to do is to make a roms folder within your Beebem folder, and in it store .bat files for each game using your choice of the beebem command line parameters. This is mine for Repton:
c:\emulators\beebem\BeebEm repton.ssd -FullScreen
Then tell Mala that Beebem roms are stored in this new rom folder (not the place in my documents where Beebem puts disc images), tell Mala that the roms are .bat files, and set your command line parameters as: %path%\%rom%.%ext%
Ta-daa!