Disclaimer: I have very little knowledge of the Active Directory - Direct connector.
From the Active Directory connector guide, in the “Domain Settings” section:
(Optional) Enter the Servers information for the domain controller servers that you want to configure using the following format:
IP AddressorFQDN. To configure multiple servers, enter a server and then press the Enter key. If you have configured two or more servers and the connection to the first servers fails, the source attempts to bind to the next domain controller server in the list.
If I am understanding your scenario correctly, you have one Active Directory forest and multiple domain controllers.
Therefore, I believe you should have just one entry in the Forest Configuration section and then for each domain, you should specify the IP addresses or FQDNs of the domain controllers that manage that domain.