You would add them to the LDIF file (or a separate LDIF file loaded after this one) -- See the LDIF format description for syntax & valid fields for the
Organization object class.
Adding a new top-level domain is done the same way as any other object, but is administratively a bit more complex: You can do it, but it's "funky" from a view standpoint because it means a new LDAP base (your LDAP tree will have two logical "roots" -
newdomain, and you have to be aware which one you're using as the LDAP search base or you'll be in for some confusing results).
If the domains are logically part of the same organization you may want to root your directory at an
Organization object & put the Domain Components under it (This is a little odd since usually you pick Domain or Organization style structuring, but it's still a valid structure. Just document the "Why" :-)