Here's how I did my multiple installs:
1) Make a fresh install of FS9, update it to FS9.1. Install any addons that you want to use in all your installs....in my case that would be the HDE Clouds package and the one file for Rhumbaflappy's mesh.
2) Create the new folders for you other installs, giving them names that clearly define the type of install that is contained in that folder: Golden Wings GA, Golden Wings Military, Helicopters, Super Sonic Jets, etc.
3) Open the stock install main folder so that all the folders and files in that install are visible: Add Ons, Aircraft, Gauges, Effects, ect. Go to EDIT, Select ALL, COPY.
4) Then go into the new folders and hit EDIT, Paste. All the computer to paste all the folders and files into each new install folder.
5) Go in and rename the FS9.exe in each new install to something unigue to each install (Jets, GWGA, GAMIL, HELOS, etc). Then right click on the newly renamed exe file and send to desk top (create short cut).
Fire up each install, adjust your setting, install scenery and aircraft.
Easy as eating too much on Thanksgiving Day.
Tim