Another question...what is the proper location for the Add-on Manager - C:\Program Files (X86) or C:\Program Files where the Prepar3d v4 files are located?
There's no "proper" location, since it will work from everywhere. But of course, the suggested default choice, which is C:\Program Files (X86)\Addon Manager, it's usually the most sensible choice, and the only reason why you want to change it, is if you don't have much space left on C:
Installing into an entirely different drive it's perfectly fine so, for example, if you choose D:\ the installer will install everything into D:\Addon Manager
Installing INTO the same folder of the simulator, it's probably the worse possible choice, since you'll lose the ability to uninstall the sim entirely and reinstall it without having to reinstall the addons this way.
Of course, when I say "without having to reinstall the addons this way", I only mean the GOOD addons, those the use the P3D installation way properly, and can install everything outside the sim main folder, and all the FSDT ones are like this. But if you force the installation to go into the sim, you are basically transforming the FSDT well-behaved installer (one that installs outside the sim), into a bad one.
My biggest problem is when I install the airports I'm not seeing any structures, etc.
Of course you have a structure: it's all nice and tidy inside the Addon Manager folder, without polluting your sim folder with stuff.