Manage domains and subdomains between multiples app engine/compute engine instances

You're able to manage domains and subdomains between multiples App Engine/Compute Engine instances. It's quite broad question, but it general you can follow steps below:

1. Register domain names using Google Domains or other registrar.
2. Decide which DNS hosting you prefer: provided by registrar or Cloud DNS.
3. (in case of switching to Cloud DNS) Create new zones for your domains (you can follow Quickstart for Cloud DNS).
4. (in case of switching to Cloud DNS) Update name servers at the registrar side for each domain.
5. To determine how many projects you need have a look at the documentation Creating and managing projects to find more details:

   Google Cloud projects form the basis for creating, enabling, and using all Google Cloud services including managing APIs, enabling billing, adding and removing collaborators, and managing permissions for Google Cloud resources.

6. Using App Engine or/and Compute Engine depends on your use case and preferences:
   • For Compute Engine you can reserve static external IP addresses (if needed), create VM instances using them and add required records to zones.
   • For App Engine you can follow documentation Mapping Custom Domains, as it was suggested by @N Singh.

Please provide more details in your question or post a new one if you need more detailed instructions.