My first thought is that the accountant works for you and he should be the one explaining what to do, but...

From what I understand, money that moves from the checking account to the reserve account, and visa versa are transfers.  Payments should only be made from the checking account.

I'm not sure what he means by zero out.  But as I see it, a transfer from reserve to checking should zero out when put against the payment.  In other words do not transfer more than the payment to be made.