I'll start by saying I'm a huge fan of PRTG I've implemented it wherever I've worked and it has only improved over the years.
I've done a write up here:
that may help other users with some of the basics and some more advanced problems that I've come across.
This will be a living document too that I plan to constantly add to and update as my current PRTG installation evolves. So this is technically not a question but maybe something to add to the wiki if there is a section for user guides and implementations. Anyway, I hope it helps someone!