If you edit a specific game (Esc+Down by default) you can customize the command line that gets run. That's probably the easiest way to handle it.
Alternatively, the rom list actually is what contains the emulator profile that runs (open the rom list in a text editor, you'll see the third column is "mame", this refers to the mame emulator in your emulator list.
sfexa;Street Fighter EX;Mame;sfex;1996;Capcom / Arika;Fighter...
sfex2p;Street Fighter EX2 Plus;Mame;;1999;Capcom / Arika;Figh...
sf2ce;Street Fighter II': Champion Edition;Mame;;1992;Capcom;..
You could set up a second "mame" emulator (say altmame), and go through the rom list and change the ones you want from mame to altmame. If you are really talking about modifying 50 games it might be faster/easier than specifying 50 custom command lines.