On a large scale for all internal stuff you are going to have your own, internal root and intermediate CA. The root CA signs the intermediate CA, the intermediate CA then signs SSL/TLS certificates for your internal infrastructure things.
As an example for a mid sized ISP with such a setup, the internal ticket portal for the NOC is accessible only while physically in the office or when on the VPN, speaks TLS1.2 only to standard web browser clients, and its URL is https://portal.tickets.burrito
where the "burrito" is obviously not the real name, I've changed it for this example, but the choice of TLD in your own internal DNS infrastructure is totally arbitrary.
Then the individual clients all have the public certs for the internal corporate root and intermediate CA installed in them, so that they trust certificates signed by the internal CA.
If you're big enough to care about having a serious multi-state-scale intranet, you probably don't want to be reliant upon external CAs to sign your stuff. Having your own internal CAs lets you do a lot of other things as well, without additional cost, such as sign per-client-device certificates as well.