Yes.
Do note however, that FolderEnhancer uses it's own folder database and not the database Apple normally uses to keep track of what's in a folder. When jailbroken and you put apps in folders, FolderEnhancer keeps track of that. If you go in to Safe Mode for any reason (or No Mobile Substrate Safe Mode) then you will see the last state of your folders before you started using Folder Enhancer - because Springboard is now using Apple's folder database.
This may be disconcerting if you've rebooted your phone but have not used the app to rejailbreak yet.
Just making you aware of that so you know what's going on if you start seeing apps in the "wrong" places.
Here's what I mean…
Normal, with Folder Enhancer working.
Safe or No Mobile Substrate Mode (probably also non-jailbroken on a rebooted 9.3.3 device).