any resources on best practices for laying out projects?

You should check out https://www.pulumi.com/docs/intro/concepts/. There is a lot of useful info there about various inner-workings of Pulumi and also about organizing projects. However, do note that there is no one solution to organization projects. That link should have a lot of info nonetheless.

Currently Pulumi Inter-Stack Dependencies approach still have some problems, ex. https://github.com/pulumi/pulumi/issues/2309 or https://github.com/pulumi/pulumi/issues/2522