The FSX Steam Edition page on the Steam website includes the following comment: "If you already have MSFSX Gold Edition installed on your PC and are concerned about running the two games alongside each other, you may wish to consider installing FSX: Steam Edition on a separate PC.

If you have the original boxed version of FSX installed at the time you install FSX Steam Edition then FSX:SE will create its own separate versions of important files such as FSX.cfg, Dll.cfg etc which can cause installers problems when you are adding third party products.  

NOTE – uninstalling the boxed version after installing the Steam version will not reset these paths back to the original Microsoft version. Nor will reinstalling the Steam version after removing the boxed version if the boxed version was originally present when first installing Steam.