Yes, and you can change the command line too, if you want special configuration, you can't change the frontend apparence (except the other theme from supporter edition) but for the emulator it s totally customisable, and you can use special script coded with autoit for "vicious" emulator.
The xml configuration look like that
<System>
<Name>Arcade Cave</Name>
<AppPath>F:\emulateur\arcade\Cave\MaMe\mamep64.exe</AppPath>
<RomPath>F:\emulateur\arcade\Cave\MaMe\roms</RomPath>
<SnapPath>F:\emulateur\mame\snap</SnapPath>
<VidPath />
<Emu selected="0">
<Cmd id="0" name="MaMeCave" value="-rompath "%path" %file%ext %volume -skip_gameinfo -nowindow" />
<Cmd id="1" name="FBA" value="%file" />
</Emu>
<Extensions>.zip,.7z,.chd</Extensions>
<Active>True</Active>
<Script>False</Script>
<Database>True</Database>
</System>
But most of the line are modified by the mgalaxy_runaway application.
The procedure is explain here >
http://www.mgalaxy.com/forum/index.php?topic=263.0