Media Directory Structure
This is a simple diagram of what my media directory currently looks like, mostly for reference because I CRS.
/mnt/media/
├── books ← Live Content
├── books ← Container Backup Storage
├── movies ← Live Content
├── music ← Live Content
├── templates ← Container Template Storage
├── tv ← Live Content
├── dump ← Container backups
├── templates ← Container template storage
├── nzb/ ← NZBNZBGet Directoryworking folders
│ ├── queue
← NZB Que Folder
│ ├── scripts ← NZB Scripts Folder
│ └── tmp
← NZB Temporary Folder
└── qbit/ ← QBitqBittorrent Directoryworking folders
├── downloadsdownloads/
←│ QBit├── Downloadsradarr
Folder│ ├── sonarr
│ ├── lidarr
│ └── readarr
└── tmp ← QBit Temporary Folder
I found that this provided sufficient separation of content and working directories for the *arrs so they did not complain. Set yours up how you want and do what works for you!