Basically, here is my structure :
/
--- /docs
--- dendron.code-workspace
--- .gitignore
--- (a folder for each of the vaults I've setup, one for work, one for personnal stuff, the personnal is added to the .gitignore)
--- /projectA
--- dendron.yml
--- (other project files)
--- /projectB
--- dendron.yml
--- (other project files)