A method for use with an internal combustion engine having both donor and non-donor cylinder groups includes: injecting a fuel in one, or both, of the groups; injecting a second fuel in both groups at a first substitution rate; recirculating an exhaust emission from the donor cylinder group to both groups; combusting a mixture of air, the first fuel, the second fuel and the exhaust emission in both cylinder groups; and lowering the substitution rate of the second fuel in one, or both, of the cylinder groups. Other methods of controlling an engine and a system are also disclosed.