I think you'll still need to use the special fork they have with the download. If you look in the installation directory you should see the special version of cgminer.

Then I looked at where it installed it on my machine:
C:\Program Files (x86)\Broadeng\DualMiner

In there should be a directory called:
cgminer-win-32bit-2014-01-24_154358

That's the version, that I used to get it to work from command line.

To make it easy, I just modified one of the existing batch files which was already there

cgminer.exe --scrypt --lo -o stratum+tcp://us-east.multipool.us:7777 -u dmpotter.dual -p x -S //./COM22 -S //./COM23 -S //./COM24 -S //./COM25 -S //./COM26 -S //./COM27