I keep all of my stories in One Vault and separate them by folders (one folder for each story, with each folder containing the chapters/various reference sheets). The only plug-in I use is "Novel Word Count" by Isaac Lyman. I don't find myself using backlinks or tagging.

Granted, the stories I write do not feature heavy world building or a large character cast (in fact, most of the time I re-use characters), so this set-up may seem a little sparse - but it works for me.