Hello, crystal-underber. 

It's my pleasure to guide you with the steps on splitting deposit and how to clear them from overdue in QuickBooks Online.

Through the Banking page we can split the deposit from there. 

Here's how : 

1.  Go to the Banking menu, then select the account where the transaction was deposited. 
2. locate and click the deposit, then select Categorize and click the Split button. 
3. Click Add lines to add more lines since you will be splitting the transaction.
4. Enter all the details including the amount and payee and its category. 
5. Click Apply and accept.

Then Undo the deposits, and create an invoice to match the deposit. Deposits added directly to an Income Account in the bank feed don’t show up in the Sales/Customer transactions list. Doing this will clear overdue deposit.

I've added this helpful article in case you need to reconcile an account to compare each transaction on your bank statement with transactions entered into QuickBooks.

Come again should you have additional concerns. I'll be around to guide you some more.