PTC's recommendation (after much discussion) was to place an additional publisher at the remote site. There are some settings you can add that will allow data checked in at a remote site to be published by a publisher also connected to that remote site. When the scheduled synchronization happens both the primary cad objects and the published representations will be copied back to the master.
I am running with a single master. If there was a master at the remote site (for certain content), then the content would stay there unless there were replication rules to push it somewhere else.
PTC has published a 39 page technical brief called PTC Windchill Vaulting and Replication Planning. It does a pretty good job of explaining how most things work, but some of the recommendations don't hold true in a single master scenario. (For example, remote sites without a master should not have both replica vaults and cache vaults - they should only have cache vaults and the replication rules should point to this vault.)
