From what I have found out, JAMMA is a standard which arcade cabinets are built. What it means is that if you have JAMMA cabinet ready, any arcade board which is JAMMA compatible will be able to use the cabinets VIDEO, JOYSTICKS and COIN mechanisms. I personally have a NEO GEO arcade board which has JAMMA connector, so if I install this board in JAMMA cabinet I will be able to use joystick and video w/o any conversions.
As for switching games, normally you would buy new MB/game. In NEO GEO's case, you only need to buy MVS game cartridges and you are ready to play.
In near future I will post some pics on how I converted my NEO GEO to play w/o arcade cabinet.
I wouldn't advise this. The Neo-Geo boards are almost the same, but you will blow out your on-board sound if you just plug it into a JAMMA cab and try to play. I know you said you'd have joystick and video which is true, but you will fry some sound components. I have a MV-1 board I just acquired that's proof of this.