If you used certbot interactively, you should be able to run it and pick just the names you want in one certificate, then again for each additional certificate. The automatic renewal step will still process all the certificates in one go, so only the initial step of picking which names are in which certificate requires running it several times.
If you use it manually, just invoke it once with each separate list -d domains for each certificate you wish to issue.
There isn’t a mode where you pick all the names once and it makes them into separate certificates based on whether they’re part of the same “domain”, but if that’s a really popular idea maybe someone could create one.
Hope that helped, and wasn’t too vague.