If you wish to manually install the scom agent on a domain controller you need to also manually install the OOMADS component.
OOMADS is an additional piece of software that enables the SCOM Agent to fully utilise the AD MP functionality. If you deploy the SCOM Agent via the push method from the SCOM console this OOMADs component gets installed automatically. If you install the SCOM Agent manually you also need to install OOMADs manually because you need this component on your Domain Controller for it to be to monitored properly regardless of what configurations from the AD MP you choose.
The scom agent and OOMADS.msi can be located in the following directory on your management server
Note if you are still running 32bit replace amd64 folder with x86
Allow the scom agent on your DC to act as a proxy and discover managed objects on other computers (This can be done via the Administration tab, Agent Manged view, right click on computer hostname, Properties, Security Tab and put a tick in the Agent Proxy box)
The action account needs Local System permission on the DC for it to function properly