Reading GraphicArts posts again, I'm assuming he started Supermodel by dragging and dropping the ROMs onto Supermodel.exe. The web site has step-by-step instructions, with screenshots, for how to install and run Supermodel here. Follow them carefully, including the part where it says to place the ROMs in the same folder as Supermodel, otherwise "supermodel daytona2.zip" won't work.
Advanced users can place the ROMs wherever they'd like, of course, and just need to modify the file argument to Supermodel appropriately (eg., "supermodel \roms\scud.zip").