My main domain is xyz.edu.pl, which have been connected to googleapps. Is it best to connect the IP and SMTP to the same domain and a different one e.g.: xyz.email?

EmailLabs is an external infrastructure (SMTP), which can integrated with your send out system, not a domain. After integration is complete you can set any domain, from which the send out will be realised. There is no need for any further integration with EmailLabs.