Use the File menu to set your MAME exe location, ArcadeVGA.txt location (it will be in the Res. Tools installation folder), and your MAME INI path,
Then check the settings are ok in the Resolution Selection' menu,
Hit 'Auto-Select MAME Resolutions',
Now hit File > Generate INI File(s).
It should stick a load of files into your ini folder, which will be used by MAME when you launch a game. Just make sure your INI folder is started correctly in your mame.ini file.