Hello @Just_Two_Cat_In_ABox
Welcome to the community!!
So looking at the input below is your idea?
/etc/filebeat/
│
├── filebeat.yml  (Main config - minimal, upgrade-safe)
│   ├── filebeat.config.inputs:
│   │     path: inputs.d/*.yml
│   │     enabled: true
│   ├── filebeat.config.modules:
│   │     path: modules.d/*.yml
│   │     enabled: true
│   └── output.elasticsearch / logging / other global settings
│
├── inputs.d/     (Custom input configs grouped by project)
│   ├── projectA-inputs.yml
│   │   └── filebeat.inputs: (e.g., log paths, processors)
│   ├── projectB-inputs.yml
│   └── projectC-inputs.yml
│
├── modules.d/
│   ├── nginx.yml       (enabled: true)
│   ├── apache.yml      (enabled: true)
│   ├── system.yml      (enabled: false or true)
│   └── other modules...
Also can review below post :
Thanks!!