Are there any resources out there that talk about managing projects & stacks using the automation API? I’m working with the S3 backend and struggling to determine whether to create multiple stacks under the same project, or multiple projects, or some combination of the two.

It should follow the same pattern as you'd use for normal projects 🙂 If it's the same resources to different environments: use stacks. If it's different resources, different deployment schedules, different reasons to destory... use different projects.