@ecterrab thank you for your reply.  I'm still having some issues with replacement, even after using Library:-SubstituteOperator.  It is unable to substitute B[2]*A[1]-> A[1]*B[2] in the expression B[2]*B[2]*A[1].  

In addition, I realized the quantumoperators have another property I do not want: it seems, by default, that Commutator(B[m], B[n]) = 0.  

How can I 'remove' this commutativity, so I don't get, e.g., B[1]*B[2] - B[2]*B[1]] = 0 ?

Thanks for the tip on attaching notebooks.  I've done so here (I hope) with my questions included:

Sub_and_commuting_questions.maple