You should test your merged Site #1 system to make sure it is operating correctly.
Search the Address Book for users who were in the old Site #2 to see if they are now being displayed for the newly-merged Site #1. Also search the Address Book for users who were in Site #1 before the merge to see if they are still being displayed.
Send a test message from the primary domain to the new secondary domains (merged from Site #2) to ensure that message routing is working correctly.
After you are satisfied with the operation of the merged system, you can merge the next system by starting with Section 9.0, Planning the Merge. If you have already completed the planning worksheet for the next system to be merged, continue from Section 11.1, Creating External Domains for Both Systems.