I don't understand.... the HDHomeRun is a tuner, it receives ATSC digital (unencrypted) broadcasts from your antenna (say), picks the channel based on what LMCE sets the channel to and transmits the digital stream to the Media Director for displaying. It doesn't have anything to do with a STB or Satellite box. It is a STB in its own right, if you like. Only difference is it sends its output over ethernet rather than s-video, HDMI or whatever. And it doesn't do encrypted channels - Free To Air only.
If you also want to receive encrypted channels from your STB or Sat, then you can add those in parallel, and use IR to change their channels, but they are distinct - the homerun does not control them nor vice versa, they are all doing the same job but for different channels.
If all you want is Free To Air ATSC channels, use HDHomeRun as 1) it is controlled over the network (no IR) and 2) it can pipe the video stream over the network.
If you do want encrypted channels, you will need to use your providers box (unless your provider allows you to decrypt on your own hardware) and control it with IR. You can then either feed the output directly into a TV and again use IR to allow LMCE to select that TV input when necessary, or if you want to be able to send the video to remote MDs you will have to use an analogue capture card to take the content into LMCE so that it can feed it to other locations.