Once you obtain the system model G, you can call any input-output pairs as you like as if you are dealing with matrices.
outputIndex = [1 4 6];
inputIndex = [2 3];
sys = plant(outputIndex, inputIndex);
When you call the plant(i,j) in MATLAB, i represents the output index and j represents the input index.
In your example G(1,1) gives you the dynamics from 1st input to 1st output whereas G(3,4) gives you the dynamics from 4th input to 3rd output. If you want to close the loop using a subset of input-output pairs but still want to have access to all the channels, "feedback()" function gives you the option to define those channels.