Haven't used the stock app in a while, but I know on Go SMS, if you go to the Notification Settings, at the bottom are options for Sound On Calls, and Vibrate on Calls. I have vibrate on, so it does do that while in a call. But the other option would logically sound your notification while in a call (haven't tested it, but I can only assume it'll work as it says it will). I don't see anything right off, so it might not be possible with the stock app.