You are thinking too hard, stop it.
You would need to make a device template for your tuner box. An example of this would be the DCT6412 device template (Look in Advanced > Configuration > Device Templates), this device is controlled by IR, and can be selected via the Setup Wizard.
Once you've gotten a USB UIRT (http://www.usbuirt.com/
), you can create a new IR device template (Select controlled by IR when it asks you), and proceed to lay out which buttons you actually have on your satellite box remote. You can then use the Learn function for each one of these codes, and Test each one to make sure it works correctly.
You also need to make sure that you have LiveTV selected as the input it provides.
Once this is done. You can then start the setup wizard. Select your new satellite box from the list (after you've selected the appropriate manufacturer), and specify WHERE it is plugged into your AV equipment and how. If it is plugged into a tuner card, you can specify it in the next screen, as well.
Once this is done, all the necessary plumbing will be done. It really seriously alarms me that people do not understand this system and think that they have to rip everything up to accomplish what they need to do.