An apparatus is disclosed, including an exhaust conditions module structured to interpret a diesel particulate filter (DPF) delta pressure value, a flow balance correlation, a NOx input value, and an exhaust flow rate value. A flow determination module is structured to determine a flow imbalance value in response to the DPF delta pressure value, the flow balance correlation, and the exhaust flow rate value. A reductant determination module is structured to determine a first reductant injection command and a second reductant injection command in response to the flow imbalance value and the NOx input value.