Transfer funds and bank deposits Reconcile

Hi,

I'm hoping someone has done this before, and I can get an easy way to resolve my issue. 

I use QuickBooks desktop. 

My client transfers money from checking to savings to pay his federal and state taxes.

I entered all the transfers from checking to savings.

I entered all deposits as one lump sum for the month, as an invoice, payment and deposit.

When I reconcile I see that each of my transfers are in the deposits and other credits column, along with the one lump sum for the month.

I usually select the one lump sum and select the payments and they reconcile.

My issue is I still see each transfer in the deposit column after the reconcile. 

I think I'm duplicating the deposit and funds transfers, because they remain on the books after the reconcile.

How do I correct the issue?  

Thank you so much!