I usually leave Prime to go over night while im asleep, but it won't hurt to use your PC while its running. I would say that the BIOS would be more accurate at reading your voltage, but im never sure myself. Mine is set to 1.425 and CPUZ reads it as 1.392V. Plus I've heard that the DFI boards overvolt the VCore slightly. Probably best to get a multimeter and check... but im never sure where to measure from!
I'm not sure if RivaTuners got it... but ATITool for overclocking ATI cards has a feature that tests for artifacts when you overclock, its quite useful to have. Can see at what point your card starts to error.