By all means backup your mame folder, but the only things that might change are your mame.ini and maybe the files in INI and CFG directories.
All you'll need is the Groovymame executable, everything else is the same.
Groovymame works by itself, but it works best if you also have CRT_emudriver installed with a compatible GPU (AMD/Radeon). Without the driver installed GM cannot make use of switchres to change your resolutions on the fly (best). You'll basically be stuck at fixed desktop resolution, like an LCD monitor. There will be an error message in the log about not finding the driver. But yes GM does work without the driver installed and you don't even need a CRT.
OK, GM will be at its best with a compatible GPU. But let's assume for a moment that you don't have that GPU. Let's assume that you plan to run all games in 800x600@60hz.
First thing to do is delete your mame.ini, because it is easier this way. Then run groovymame.exe -cc to create a new mame.ini. Edit it for your roms directories etc.
Then run VMMaker, which should come with the CRT_emudriver package. You'll get an error message about no driver present, don't worry about this. Go to "Edit Settings", choose your monitor type (for this example choose VESA GTF 600). Then go to the last tab "mame" and browse to your groovymame executable. Click to "Export settings to groovymame". Click OK, you'll see a message "Exporting settings to mame.ini...". Type "exit" + return to quit.
Your mame.ini has just been updated with your VGA monitor's range.
There are a few settings in mame.ini you might need to pay attention to, if they aren't already correct:
video auto
resolution 800x600@60
super_width 800 (by default this will come up as 2560, so change it to your desktop max width)
syncrefresh 0
autosync 1
autoframeskip 0
frameskip 0
throttle 1
keepaspect 1
unevenstretch 1
unevenstretchx 0
unevenstretchy 0
autostretchxy 0
intoverscan 0
intscalex 0
intscaley 0
Then try running a game like Flying Shark with:
"Groovymame64.exe -v fshark > fshark.txt".
Let it run a minute. Does the game look/sound right? Correct aspect ratio? Quit and check the log file. Did the game run at 100%?
I hope everything I said there is right, I don't normally run it this way myself, and of course I don't know the software like Calamity.
Some other useful threads that discuss related issues:
http://forum.arcadecontrols.com/index.php?topic=146397.0http://forum.arcadecontrols.com/index.php?topic=158259.0http://forum.arcadecontrols.com/index.php?topic=152498.0