I had to troubleshoot this one myself.
Here is how the antenna/cable system works.
I will use the Winegard Amp as "typical"
http://www.winegard.com/kbase/upload/2451489.pdf
Is the manual for our Amp.
Note that the Cable connection outside goes to the middle connector on the back of the unit. The External Over the air antenna from the roof goes to the left side back of the unit and the #2 TV (or splitter) goes to the right. The #1 TV goes on the front of the plate.
The SAT connection (if equipped) outside DOES NOT go through the amp but goes directly to the upper connector on the plate.
To use the roof antenna you need to turn on the amp with the little black button. A green light should come on.
To use cable you MUST (no Kidding MUST) turn off the amp. If the green light is on the cable will not work.
Hope this helps.