You should be fine running the combination you have. If the Onkyo can select the impedance for each output, you should tune it accordingly. I suspect it is a setting for all speaker outputs, and would recommend setting the system up, with speakers connected and testing with both. You probably will/should set it for the majority of the speakers impedances - 6+.
You may be suprised at this, but the weakest link are the Yamaha speakers. The Definitives are decent, and the Vega is ok. I make this statement without knowing the model numbers of the pieces. The only piece of musical gear from Yamaha that I would recommend is a Baby Grand Piano.
Your choice of the Onkyo is made, so we will bypass that. You may notice a change in vocal quality as the voice progresses through the speakers ( centre=>fronts=>rears) The main benefit to geting a matched set by one manufacturer is they should be matched for tonal quality and balance. The voice should not"smear" or change tone when moving around the spectrum.