aircraft go in your "x-plane\aircraft" folder
Make sure if you are on windows vista or 7 that you do not install x-plane in the program files folder. If you already installed there, don't worry, just move the x-plane folder to another location such as c:\x-plane\
I have created a folder inside aircraft called 'Payware' and another called 'EHM' for euroharmony planes - how you organise it is up to you.