If I have 3 github repositories. Can I nest them in a prefect project, and have the deployment yaml file point to the flows in each repository? So that they can run in the same server?
I would suggest creating 3 deployments, one for each GitHub repository.
With newer versions of Prefect, prefect.yaml will contain the configuration information for each. Upgrade your Prefect version with pip install -U prefect.
You can then create a deployment by running prefect deploy from the root of one of your locally cloned repos. You can repeat for the other two deployments.
You can use the same work pool for all the deployments, if you like. The work pool lives on the server.
You can then start as many workers as you want on your infrastructure.
The docs contain tutorials and guides on the updated experience with deployments and workers and work pools.