A little late to the party, but I'll explain how I do it:
i) I use FARR to launch, and have a couple of directories with links to tools (to make FARR run faster)
ii) When I want to search a file, when i remember part of the name, i use everything
How would I like FARR to index? Easy, I would love if FARR scanned the directories configured on startup (or maybe a subset of them, a check to cache...) so my tools folders would allways be indexed and work blazing fast, and when there is no match (or I dealy on clicking) it'll keep on searching on other folders...