How do you handle cases where you have users in O365 (Exchange Online) using Domain2, and other users in Exchange On Prem (using Domain1)?
For starters, read this:
https://technet.microsoft.com/en-us/library/mt491268(v=exchg.150).aspx
Here are the scenarios:
Scenario 1 MX record points to Office 365 and Office 365 filters all messages.
Scenario 2 MX record points to Office 365 and mail is filtered on-premises.
Scenario 3 MX record points to my on-premises servers.
Scenario 4 MX record points to my on-premises server, which filters and provides compliance solutions for your messages. Your on-premises server must relay messages to the Internet through Office 365.
In Phase 1, we will need to consider either Scenario 3 or 4.
In Phase 2, we will move to Scenario 1.
We’ll need to find a way to transition from Scenario 3/4 to Scenario 1.