I have the exact same setup that you're describing. I bought a "Y" connector from Home Depot, and each end has a short length of hose connected. I connect one to each engine flush fitting and run them both at once. I've been doing this for years without any issues.
I guess it all depends on your main water supply though. My marina has city water and it comes out like a fire hose. But if you're on a well for instance and your flow rate is lower, then I suppose it's possible that you may have issues, but I'd say go for it.