My hdhomerun dual gets a lot fewer channels than my QuadHD. Will it be used first for the channels it can get? If so, I'll remove any channels it gets weak signals on from it's list.
You set the priority of tuners on how the are used for recording and live TV. If you merge tuners and one isn't available that doesn't cause a problem.
Priority would be how they were detected using HDHR discovery. Live TV is reverse priority to save quality for recordings but there is a config.xml setting to use recording priority.