To solve reports, after properly adding the vendor credit per the link below "enter a refund from a vendor", I had to delete the manually added deposit so that there was only the actual bank deposit added from banking matched to the vendor.
After taking care of the duplicate deposit I had to go into the vendor expense table, by selecting it from the vendors tab, and made sure the blue "online banking matches" deposits were the only ones there and that the "accounts payable" was the account the deposit is linked to.
Working with multiple vendor credits and deposits at the same time made things a bit tricky by applying partial vendor credits to a particular deposit. Once I had properly gone through the initial "pay bills" screen I had to hit the refresh button to make the "bill payment" populate so that I could properly allocate funds from the vendor credits to the corresponding deposit. BE CAREFUL. This can be easily missed as there is no way of knowing that the funds are not allocated correctly without physically going into the "bill payment" after the initial "pay bills" screen.
Occasionally an additional refresh is required to correct the "open" or "overdue" bills.
Thank you to all that helped me take care of this issue. Hopefully this explanation helps another.