The frontend doesn't really do anything. There are no options to input command lines anywhere. Command lines are gay. I wonder if the programmers have upgraded from DOS. They probably don't even understand the concept of a GUI. And again, I bet they have glasses and/or ponytails.
Please... your not a programmer, so quit talking out your ass. If you're too afraid to use a command line interface, then use Ootake(free) or ME($$).
Mednafen isn't a DOS app, it's a console app of which its source is portable and compilable for many OS systems including MAC and Linux boxes. It's also an extremely easy console app to use. If you want to run CD games, you need to open the mednafen.cfg file, locate the "pce.cdbios" string and change is to "pce.cdbios c:\pce\roms\syscard.pce" or whatever path *and* system card rom you're using. You can also setup the window and fullscreen res options in this file.
Once that's done, you can load CD games from the command prompt with: mednafen -loadcd pce. If you're using ISO/CUE/WAV sets, then: mednafen <filename>.cue. You can also drag and drop CUE files onto the mednafen executable file as well as other roms.
In the emulator: alt+enter switches between fullscreen and window mode, alt+a steps through the game one frame at a time and alt+r returns back to running normal, F9 saves snapshots to the snap directory, F5/F7 is savestate and loadstate, F10 is a hard reset. To configure a gamepad press alt+shift+1 and it will bring up the gamepad subscreen at the bottom. If you mess up, press alt+shft+1 to cancel and then again to re-enter. You can press F1 for help it you forget the keys.
Btw, two of the more recent Genesis emulators scale the 256x224 games mode to 320x224. That sucks when you're trying to get an acurate pixel capture. Some of the older ones don't do this. I use DGEN for when I need to rip lower res gfx or disable layers by priority (no other emu does this). Oh, and DGEN is a windows GUI app.
