Well,
My personal preference is to have separate file folders for each location so I can troubleshoot any potential conflicts, scenery anomalies, etc. It's just much easier to track stuff down for me.
But however people want to install stuff is entirely up to them.
It might make our time helping people troubleshoot stuff much longer though if we can't locate stuff easily because it's all grouped in one folder inside the FSX scenery library. So, customer support may suffer with that, may not.
We will see. So far, I've had pretty good help with everyone's early issues that have cropped up. I'm hoping that trend will continue.
Brad