Yes, The Geek Squad can change how your system operates. All of your Remotes act like an On-Off switch. They can be programmed to turn many devices all on or all off. This can be a problem. If you are watching a movie disc and want to watch regular TV from a cable box you may turn off both the disc player and the TV when turning off the disc player. This gets more of a pain when you have three, four or more devices in your home system. One on-off button on a device may control many devices. Remember that all of your remote controls have an on-off button. When you press it, it will turn ON the device that it is used for but it may also turn OFF another device that is already ON. Explain this to your Geek Squad rep. He may be able make changes on your remotes so that you have more control of your devices.
Nick