You can have multiple MAs connecting to the same store. It's just a configuration in the StoreOnce gateway option (add more gateways). I believe the whitepaper lists this option. The MA function is independent of the StoreOnce software (SOS) function.
You can use source-side (client) or server-side (dedicated MA) deduplication on location A and then transfer the data to location B. Or, if you feel the bandwidth is still not sufficient, setup a StoreOnce store in location A and then perform object copy to location B.