You can order Metal Mule pannier frames in 2 styles: 

There are "Offset" frames which have an offset to one side to clear your bike's exhaust system.  This results in one pannier being offset from the centerline to accommodate the exhaust.  For that reason you may want one pannier to be smaller than the other.
 
Or there are "Balanced" frames. These frames generally require a Metal Mule exhaust system which is narrower than the stock exhaust on your bike.  With a Balanced frame your panniers will be symetrical on both sides, and both panniers can be the same size. 

Select the frame for your bike, provide us with specifics, then go to panniers.