Replication between two existing databases

we have two existing database with exactly same schema in two sites.

now trying to use SQL 2012 to merge few tables between these two DBs.

obviously, can't use snapshot to initialize the replication as the subscriber will be overwritten by publisher's data, which we don't want and of course, can't use Backup for the same reason either.

would this really be possible? what we need to use to initialize the replication then?

or, we have to manually merge those tables from each DBs to have all rows before the replication?

any thoughts and suggestions are very much appreciated.