Oh, I ran fusion without command line parameters and it seemed to work fine? At least the one I tried did (it was an SMS game IIRC.)
Anyway, the idea is that you can create your own profiles or templates, so you don't have to remember or mess around with the countless different command line options (if any) of certain emulators.
A step I'm thinking of is adding a very simple frontend, which allows you to link folders to profiles, so you would create a profile FusionSMS and link it to a folder with all SMS files, and a profile FusionGEN for all genesis files. Nothing too fancy, but with the current profiles in place it's rather easy

Profiles, btw, are supposed to be user defined profiles for his / her applications. They can be easily picked in the combo box on the Profile tab.
Templates are applied to one or more tabs, and use the files stored in the Templates folder. The file format is identical.
Remember, command line support is still missing, but the idea is to do something like:
UniRun FusionSMS game.rom
... yet with folder linking I might let you get away with just specifying the rom file, food for thought, food for thought...