I go the folder structure route. I use multiple kali vm’s for different purposes. Each has the root user’s home managed by git that I push to my server. For htb, I use a folder for each box. Notes are in a readme.md file. Scripts, command output, and loot are stored in the directory. I also use script a lot when getting shell on boxes so it logs my tty session to a file in the box’s directory. And I use scrot bound to keyboard shortcuts auto grab screenshots and put them in the right folder.
I like this setup because it helps to quickly sync vms between my workstation and my laptop, or kill off a vm instance and bring up a fresh new one, and backups are included in everyday normal operation.