Honestly I have never used the predefined muxes, I always add each mux (ATSC channel) manually.
Go to TVFool.com and enter your address to find channels in your area (start with the ones in green)
Note the channel numbers in the Real column. These are the channels that the stations are actually transmitting on.
Go to https://en.wikipedia.org/wiki/North_American_television_frequencies and look up that real channel number. It will show you three frequencies for each channel, none of which is the one TVHeaend want to see. So, take the Video carrier frequency and add 2.03. For example, Channel 8 has a video carrier frequency of 181.25. 181.25+2.03=183.028. Now take that figure, remove the decimal point, and add the digits 615 at the end, so in the case of Channel 8 the number becomes 183028615. That is the frequency in Hz to enter in TVHeadend. The number should always be nine digits long and end in 028615.
So start with one channel and create a mux. Assuming you've already created one ATSC network in TVHeadend, go to Configuration, DVB inputs, Muxes and click Add. When the popup window appears, use these settings:
Enabled: (check the box)
EPG Scan: Disable (unless you want TVHeadend to try using OTA guide data, which is generally only available for 1-3 days)
Scan Status: PEND (IF YOU DON'T CHANGE THIS IT WON'T SCAN THE MUX!)
AC-3 Detection: Standard
Delivery System: ATSC
Frequency (Hz): The 9-digit number ending in 028615 that you computed for this frequency
Modulation: VSB/8
Click Save and it should scan the channel and if all goes well, after several seconds the scan status will change to OK and show the number of services that have been scanned. You can then go to the Services tab and select the services you want to enable and then click "Map Selected". In most cases you will only want to map services with low (1 digit) Service ID numbers because the ones with higher numbers (typically 4 or 5 digits) don't correspond with actual channels. Once the Channels are mapped go to Configuration, Channel/EPG, Channels and you should see your newly added channels, and on that page you can rename them, change the channel numbers (in case you want to show the virtual channel numbers rather than the physical ones) and so on. But before you do that I would just take a moment to verify that you can watch the channels in Kodi or whatever you are using as frontend software.
If you do it this way and it works, then you will have some idea how things are supposed to work and you can either add all the muxes manually (which I actually prefer so I don't have to deal with ones that can't receive any local signals) or you can try one of the preconfigured muxes again and see if you can get it to work, now that you understand how it's supposed to work.
Just as a footnote, if you enable the EPG scan you may see your HDHomeRun tuners come on at odd times, or maybe even stay on constantly, depending on how often TVHeadend looks for new guide data on the various channels. I prefer using zap2it to get guide data (I followed these instructions:
https://freetoairamerica.wordpress.com/2014/12/03/some-hints-for-getting-free-to-air-satellite-channels-into-the-electronic-program-guide-in-kodi-or-xbmc-or-another-frontend/), so I always leave the EPG scan disabled.