Because you're pressing the CONTOUR button, I'll assume you have either the XR11 or XR5:
1. Point remote at receiver
2. Press VOICE button
3. Press & Hold SETUP button
4. LED: green
5. Press CONTOUR button
6. LED: flashes
7. Press CONTOUR button (again, again, again) until Instructions display*
8. Enter 3-digit code
*As far as the upstairs code also displaying on the downstairs box, Cox noted the following on the page:
"The remote may attempt to pair with other compatible receivers within 50 feet. Each press of the Contour (Menu) button tells the remote to change receivers."
I believe each press of the CONTOUR (again, again, again) selects the intended box (within 50 feet) you're attempting to pair.