I got it to work finally.

:
If anyone is interested, it is kind of a process to make it work. At least it was for me.
1. The setup in the HDHomerun. Part of that entails a registry setting.
2. Backup your registry, close all open programs, open regedit, navigate to:
HKEY_LOCAL_MACHINE\Software\Silicondust\HDHomeRun\Tuners\XXXXXXXX and set the BDAPIDFilter entry to "Enabled" (no quotes, case sensitive). Repeat for the -1 tuner. I got that off the silicon dust forums.
3. To get the normal ATSC OTA channels to come in, you need to set the main application in the HDHomerun setup to ATSC Remap and scan in you channels there.
4. Set the tuner in DVBViewer options/hardware to only have two boxes ticked, and they are the has CI module, and open whole transponder.
5. Scan in your OTA channels inside of DVBViewer using ATSC and the ATSC transponder list.
6. Go back into the HDHomerun setup, and change the main application to ATSC QAM remap.
7. Go into DVBViewer, and set the tuner assigned to your QAM HDHR tuner as preferred, and tick the two boxes as above.
8. Scan in the channels within DVBViewer using ATSC as the source, and using the ATSC Cable Std.
At that point, everything should work.
I tried having both tuners set to normal, and it would switch back and forth, but the switch was slow, and sometimes the video wouldn't come in.
So what I am doing for now, is if I want to watch OTA, I go into the options/hardware settings, and set that tuner as preferred, and the others to "Do Not Use".
If I want to watch cable, I go back into the options/hardware, and set that tuner as preferred.
Hope this helps someone else in the future.
It only took me since yesterday to figure it out.
Thanks to those who responded here.