Les:

Whether the connection from the charger to the batteries is made at the battery terminals or at the output of the isolator is totally irrelevant AS LONG AS THE WIRE IS SIZED RIGHT. That wire needs to be big enough to carry the alternator's full output and the charger's full output, even though the chances of seeing that much current output are almost nil.

And don't worry about two charging sources supplying the battery at the same time. Happens all of the time and will happen whether the connection is at one end of the wire or the other.

David