MythTV has two interfaces, the backend and the frontend. The backend is the nightmare to get set up and there's a lot you have to do before you use MythTV. Detailed instructions are in the link below.
http://www.mythtv.org/wiki/User_Manualetailed_configuration_Backend
MythTV can be highly customized (as with just about anything in Linux), but with that flexibility comes complexity. The link above isn't very intuitive either, so I'll try and help out a bit. All the information you need is on the menu to the right so make sure you go through all of it to at least get familiar with it.
In a terminal type mythtv-setup
Get your General Settings done. Mainly your IP's need to be set. For one machine just keep the IP local (127.0.0.1)
Capture Cards (Those are your Homeruns. They have to be designated. Each tuner needs it's own. (Homeruns have 2 tuners I think)
Input Sources (Antenna, Cable, etc. If you're running OTA, create one called Antenna and attach your Homerun devices to it. Can't remember if you need one for each Homerun device or not.
Then you have to do a channel scan. You'll need a Schedules Direct account. It's $20.00 per year. That gives you your channel guide. You don't have to do a channel scan for each device.
Edit your channels accordingly. You can set your channels to any number you want, and in any order. However, this is a gotcha. For each tuner in your Input Sources, you have to make sure the starting channel is the same as your edited channels starting channel. For example, if MythTV scans channels and your first channel is 2.1, and you say, I don't want it to be 2.1 and you edit it to be a simple 2 instead. You'll have to go back and make sure the starting channel on each Input Source is set to 2 and not 2.1. (I've nearly punched a TV because of that).
On the Schedules Direct website you can enable and disable any channels you like so they're not scanned by MythTV. You don't want 10 channels in Spanish, Polish and Chinese. You can disable them so they never show up in your guide. Play around with it.
Run mythfilldatabase in your terminal. Then run mythbacked once mythfilldatabase is complete.
If you would like screenshots of any particular part, let me know. Once set up, it's awesome.