After a bit of pain and head scratching, I was able to query my hdhomerun prime for a list of frequencies and programs. The resulting list is a file that you can stick in /usr/local/share/tvheadend/data/dvb-scan/atsc to make it available in your "Add DVB by Location" button within the TV Adapters tab of tvheadend configuration. I have attached a list for my local Comcast. This is for the Waukegan/Lake Forest Illinois area.
Assuming you have already installed the necessary drivers for your device:
To get your devices ID
$>hdhomerun_config discover
To scan for programs/channels/frequency
$>hdhomerun_config <device id> scan 0 scan0.txt
This scan will take a few minutes, but when you are done you will have a file list every frequency and the programs/channels within the frequency. It will be of the format:
...
SCANNING: 823750000 (us-hrc:129)
LOCK: qam256 (ss=75 snq=89 seq=100)
TSID: 0x81C1
PROGRAM 1: 201 Destina (encrypted)
PROGRAM 2: 222 Discove (encrypted)
PROGRAM 6: 506 FXM (encrypted)
PROGRAM 7: 274 Militar (encrypted)
PROGRAM 9: 471 CMT Pur (encrypted)
PROGRAM 11: 26 Jewelry (encrypted)
PROGRAM 12: 406 Outdoor (encrypted)
PROGRAM 14: 473 VH1 Cla (encrypted)
PROGRAM 15: 271 Investi (encrypted)
PROGRAM 18: 418 CBS Spo (encrypted)
PROGRAM 22: 53 CLTV (encrypted)
PROGRAM 27: 75 Total L
PROGRAM 28: 119 EWTN (encrypted)
...
Where 823750000 is the frequency, under which each program available in that frequency is listed, as well as its common channel name and number.
To build the list that tvheadend needs just copy down each frequency that contains programs that you are interested in and toss that in a file that matches the format of the attached file. When your file is built, move it to /usr/local/share/tvheadend/data/dvb-scan/atsc.
You can now choose your file in the "Add DVB Network by Location" list and you should get a good mux for each frequency once the scan begins.
Once the scan is finished, pop over to the "services" tab and add a channel name for each channel that the scan found. You can use the scan0.txt file to figure these out. I found it best to first sort by the "play" column, then sort descending by the "Multiplex" column so that the list is in the same order as the scan0.txt file. This part is tedious, but you can knock it out in a half hour or so.
Once you are done you can go back to the "general" tab and hit the "Map DVB to services" button.