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
├── nzb/ ← NZB Directory
│ ├── queue ← NZB Que Folder
│ ├── scripts ← NZB Scripts Folder
│ └── tmp ← NZB Temporary Folder
└── qbit/ ← QBit Directory
├── downloads ← QBit Downloads Folder
└── 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!