I use that , the way you do it is to put all the files the same as your FSX Dir. EX: i have gauges , effects and the airplane files so what i did is that i put all those in a folder , inside the folder i put another folder named Gauges and put all of my gauges inside the folder, i created an Effect folder and put all my effects in it and finally i created a simobject/airplane folder and i put the aircraft file in it. When you compile you choose the whole folder that you created first and it point the installation to your FSX Directory . It should automatically put the files that you wnat to the folders that you pointed. If the file is there will automatically overwrite it . The picture below is the way i did it.
If you have any question please ask , willing to help you