When you download a plane in a specified folder and then unzip it , what do you do when there is more then one folder ie: aircraft , gauges effects e.t.c.  i know that the aircraft goes in the FS 9 aircraft folder , where do the other folders go ? 

The gauges, effects etc. go into the appropiate folders in fs9. For instance, if there is a gauges folder in the zip file, I open the folder, copy all the gauges, then paste them into my fs9 gauges folder. Same with effects, or whatever else is in there 

Quick tip.  Zip your gauges and effects folders when you first install FS, and leave them in the original folder.  That way if you ever have to undo your changes, you can quickly get the default files back.