I have the the Saitek Pro Yoke and Rudder Pedals. I can download a profile for FSX, but I'm not sure what it does, how it works? Does it over-ride my FSX controller settings? Or do I need to set up both independently. I guess I don't quite know what each does and how they interact together.

I do not use any components of the software. When I tried using them, there were too many conflicts and it just wasn't necessary when I could achieve everything I needed to do through the FSX/Level-D/PMDG keyboard shortcut menus. FSUIPC can probably help as well.