Unsolved Hybrid Azure AD clarification

[Markferron]

Our domain users are currently synced over to Azure using the Azure AD Connect tool. Our workstations are not synced over to Azure but we were thinking about finally rolling over to Hybrid Azure so that we could have MFA setup as a log in option for specific machines. If we make the switch over to hybrid and start syncing workstations over will that change the way all users log in? The reason I ask is that we have two domains on our O365, let's call them 1.com and 2.com, but only one domain on our local AD server (1.com). When I sync the workstations over I am worried that 2.com will somehow replace 1.com as the log in option for the machines that are on the domain on campus. Is there a way to scale the sync down to a few select users and machines to test?
For any clarification, I've screenshot our current AD Sync settings https://postimg.cc/YjqFP2QY

Appreciate any help and insight!