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
├── movies ← Live Content
├── music ← Live Content
├── tv ← Live Content
├── dump ← Container backups
├── templates ← Container template storage
├── nzb/ ← NZBGet working folders
│ ├── queue
│ ├── scripts
│ └── tmp
└── qbit/ ← qBittorrent working folders
├── downloads/
│ ├── radarr
│ ├── sonarr
│ ├── lidarr
│ └── readarr
└── tmp
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!