How do I deal with a recorded cash transaction in "Bank" A and a literal cash deposit in Bank B which refer to the same physical money?

How do I deal with a recorded cash transaction in "Bank" A and a literal cash deposit in Bank B which refer to the same physical money?

I have a Bank, Wells Fargo, and I physically deposited cash into the ATM. This cash is a lump sum of transactions that were made throughout the day. I import my bank statement into Zoho. 

I record all cash transactions on my Woocommerce WordPress website. I do this so I can collect customer data, and have a unique transaction history for each person. I import these transactions into Zoho. 

For this example Let's say I deposited $100 into Wells Fargo using the ATM. This is the total cash from a day of 5 sales. Each sale is recorded on my website as $20 each.

So.... in Zoho, I have 2 "banks" reporting $100 for a total of $200, when I only actually have $100 cash.

I need to know how to deal with this in the most legit way, so my books are balanced and the IRS won't come knocking at my door asking "What happened to the missing $100?"

1. Do I simply delete the cash ATM deposit within Wells Fargo "Bank?"
2. Is there somehow a way in Zoho to match the transactions together so they are related and one is ignored?
3. Is there any other solution you can think of for this?

Thanks,
Tim