Generally speaking, machine authentication certificates are done through Microsoft AD or similar. Group policy can be configured related to auto-enrollment from the Microsoft CA, and enforced through their mechanisms. The machine certificates are stored in the certlm console page (On most Windows computers, just begin typing certificate in and you should see Manage Computer Certificates) which is part of the CAPI store.
If you are manually installing a 3rd party certificate for machine cert, then you will need to make sure you have a way to let your DC know about the machine certificates, as access is generally defined by OU for machine-auth.