Hi Mark,
To answer your question, yes. If you don't want to constantly have to center and adjust each game you play, pick one resolution and refresh rate and stick to it. You can set it in MAME using the ini options resolution and refresh. You can set it in Mamewah using the layout creator.
I happen to run my arcade cabinet in one of two modes (1024x768 at 60hz, or 1024x768 at 85hz) depending on the game, so in my case I have two video modes to center and adjust and then all games look perfect.
Thanks!
Alan