Will the MCP run automatically or do I have to explicitly mention it in the prompt?

This depends on the client. In Clause Desktop, the MCP server will be automatically activated as soon as a connection is established. Claude decides itself when a retrieval is sensible. However, you can also explicitly (de)select access yourself. A proven approach: create one project per use case in Claude, add the relevant domain and context as project instructions and only make concrete queries in the chat after.