Here are the answers for those looking:
The command line for Sega Model 2 is:
emulator.exe %rom%
I didn't use any pre/post commands.
Customize Controls:
Once a game is running, go to windowed mode. Select Game>Configure Controls...
There you can remap keyboard controls. It appears you have to do this for each and every game for the CFG file to be created for each.
To close Sega Model 2 emulator with Mala/Quit back to Mala without showing Sega Model 2 shell:
Use hotkeys. Select "Close" on the left column. Name = Close. Now in the "Source" field where the default "ESC" is displayed make it greyed out by clicking it. This is where the change is made. Change that key to whatever you want. IE: Q, F1, etc.
If Sega Model 2 shows the exact names of the Roms in the "All Games" list, there is a fix without having to rename the roms themselves.
I figured it out with help from this thread:
http://forum.arcadecontrols.com/index.php?topic=102476.0In Mala Options main window, go to Game Lists. Choose Sega Model 2 (or whatever you have it called) from the drop down menu, then "All Games". On the right within the Games tab click "Edit Game List...Launch Mala Layout". There you can change the game names from the rom name on the right (Destination)
Alternatively, if you wanted to set up your own simultaneous 2-button close-emulator function (ie button 2 & 4 at the same time) outside of what if offered by 'hotkeys' within Mala, you could create a AutoHotKey script that might look like this:
SetWorkingDir, C:\Arcade\Sega Model 2\
Run, C:\Arcade\Sega Model 2\emulator_multicpu.exe dayton83
~2 & ~4::
Process, Close, emulator_multicpu.exe
ExitAPP
return
Doing this would require a new execution setup within Mala:
Under "Other Emu Config" place the following:
Basics tab;
Name: Sega Model 2
Executable: explorer.exe
Rom Path: (use your full path to your AHK scripts folder, NOT your ROMS folder)
Rom extensions: ahk
Execution tab;
Pre commands: (empty)
Command Line: "%path%\%rom%.%ext%" (include quotes)
Window State: Hidden (my preference)
Options tab;
Snap/Title: (full path to snaps folder. Snaps have name of AHK files)
Best of luck!!