I have never had to choose, but from what I picked up last time it will ask you to do something when you login again for first time. Please see this topic for more.
If two people, cities, or alliance have the same name
, they will all get renamed to a number like "@2523452345". This always happens, there is no way around it. Then the first player to change name of sire/city/alliance can get it again.
The epic hero timer is still going.
Side advice: Don't spend lots of time to do gear fortify or use massive hero gift for 1 or 2 days after merge, especially if there is some big problem with the map or armies. That way if they have to redo the merge we are not mad about lost progress.