Hippockets,
There must be two separate installs of FS9. What you should do first is rename the FS9.exe to FS9.1.exe.You must also do this to the Program Files > Microsoft Games > FS9 folder and to the Application Data for FS9. Once done, reinstall FS9 once again and on the second install, rename the FS9.exe to FSGW3.exe. Do this for the newly installed FS9 that is now in your Program Files > Microsoft games folder and also to the Application Data folder; renae all FS9 folders to FSGW3. Open the renamed FSGW3 in the Application Data folder and rename the FS9.cfg to FSGW3.cfg, then go back and rename all the FS9.1.exe (desktop, Program Files, and Application Data) to the original FS9.exe. Now you are ready to install FSGW3 into the FSGW3 Folder. Do not worry about the Applicatiob Data, it will rewrite itself once FSGW3 is installed in the proper folder.
BTW, all of the FSGenesis 38-meter DEM mesh works in FSGW3 just as well as in FS9, you just have to direct it to the FSGW3 folder. I would not advise using GE-Pro or UT with FSGW3.
Hope this helps,
Caz