What version of PMS are you running? To use multiple boxes, unless you are using 1.9.3 (or a really old 1.6.1), it’s not going to work. If you are running 1.9.3, keep reading. If not, upgrade.
Since you are using the same EPG for both boxes, what you can do is disable the channels that don’t work on each of the boxes. I have 2 HDHomeRun Connects connected to 2 difference antennas. ABC (the only VHF channel in my area) doesn’t come in very well on one of the antennas so I disabled 8.1, 8.2, and 8.3 on one box so that Plex would not schedule any of these channels on the “bad” box.
Using the device’s web page, I went thru all the channels and marked as favorites (yellow) the ones I wanted and disabled (red X) the once I didn’t want. Occasionally new channels would pop up and these would not have a color associated with them. This way I could identify that a new channel was added and decide if I wanted to keep it (make it a favorite) or didn’t every want it (disable it).