Vaults are a central part to Structured Tree. Each Vault is simply a folder with notes inside them. Structured Tree does NOT go into subfolders, so any notes in a subfolder of a selected vault will not be detected. Due to this, it's recommended to have all your main notes inside a single folder.
Multiple Vaults show up as different top level (root) notes. Below is a picture of a setup with the main vault (Home) and a secondary Vault for Readwise exports
https://github.com/user-attachments/assets/7fb6991b-04ca-426c-ab09-01be08e7e234
To add a new Vault, go to the plugin settings, click "Add Vault". Select the path of the folder and the desired name of the vault. These do not have to be identical
https://github.com/user-attachments/assets/c9e464ee-158a-417b-b531-6c02c35738c0
To remove a Vault, go to the plugin settings and click "Remove" next to the Vault you want to remove. This will NOT delete the folder or any notes within it. It only removes it from the Structured Tree view.
Using backlinks (in Obsidian [[]]) between different vaults is a bit clunky at the moment. If you try to click a backlink to another vault, it will create a new file with that name in your current vault. This will be improved in the future.