Using one dimmer to control 2 sets of lights with each an On/Off Switch
Yeah that's fine, have a master dimmer then 2 switches deciding which LEDs are on.  

However the LEDs and the dimming method must be compatible. Generally with 12V you use PWM dimming.  Make sure you select LED lights which are friendly to PWM dimming, i.e. Have a simple resistor regulator instead of a switching power supply.  If the bulb says "works on 12-24V" it's a switching power supply type, which will treat attempted dimming as dirty power, and attempt to compensate for it. 

IKEA comes to mind as a source for architectural grade LED fixtures made for PWM dimming.