In the game mapping you can select individual engines (shift_1 for select engine 1 for example). On my CH Pro throttle I have the left finger button for selecting left engine, the right for the right, and the center button for select both.
So, if I am running both engines at military power, and I press the button for the left engine, and change the throttle, or RPM settings, or press E...only the left engine is affected. The right engine stays at military power.
And yes, AH controler mapping is very flexible. You can set a quad up for 4 engine operation, and the levers for engines 1 and 2 will still be the same for twin engine planes.