I keep a documentation page in my wiki for every thing I set up - how I did it, what I ran into, how I fixed it, and where everything is. Reason being, when it comes time to upgrade or I have to install it again someplace else, I remember how I did it. Basically, every completed step gets copy-and-pasted into a page along with notes about it.
As for watching the file system, I have AIDE on all of my boxen (configured to run daily, but not configured to copy the new AIDE database over the old one automatically). That way, I can look at the output of an AIDE run and see what new files were created where (which would correspond to when I installed the new thing).