There is no solution, it is how you're viewing the problem
that needs to change.

The Replication Manager window is able to differentiate
between the two, it just has one replica's view of the
replica set open at a time. Ie. What other synchronizers
and unmanaged replicas it knows about and their screen
layout. From the File->Manage Replica option, you will see
one replica highlighted. This replica is the primary
replica that the synchronizer uses. So on the screen you
see what it's view of the replica set. To test and
understand this, again go to File->Manage Replica and
select the other replica and click open. You will likely
see the icons layed out differently; it's view of the
replica set.

So how it works is that the synchronizer replicates data
from the Primary managed replica to all the other replicas
it manages, and also replicas data from the primary
managed replica to another syncronizer's replica. (usually
the other sync's primary replica, from what I've seen. But
from what Michka has said, the other synchronizer chooses
which replica your synchronizer replicates with.)