Not sure about Q5. But I have done double mutations with 2 pairs of primers using Lightening mutagenesis kit (Agilent). I picked two clones: one with both sites mutated, the other has single mutation. I will recommend to try multiple sets at first running. Worse by worse, you should get single mutation clones. Good luck!

Thanks Zhejian. Yes I have tried multiple primer sets with Lightening kit too. Just wondering if Q5 can also be used for that. Q5 is pretty efficient in my hands (more so than lightening) so just wondering