I have 2 seperate invoices for the same customer with deposits made on both. 1 says payment received but not deposited so it won't apply it. It's also combining invoices.

Resolving your situation depends on whether the payment was manually entered or deposited to your bank linked to online banking in QuickBooks, toddvu. I'll provide the steps for both scenarios below.

We don't have to combine invoices or separate the payment to rectify your concern. To clarify, is the deposit coming from the Bank transactions page? Was it just a single transaction with the value amounting to the two separate invoices?

If so, we can match that entry to both invoices:

1. Go to Transactions, then Bank transactions.
2. Locate and click the deposit from the For review tab.
3. Hit ◯ Match.
   
4. Modify the From and To fields to show accurate entries.
5. Click the Checkbox for the designated invoices for this deposit.
6. Once done, tick Match.
   

    

However, if you've manually recorded a single payment for both invoices but only applied it to one, the exceeding amount will automatically be converted into a Credit once saved. We can link this entry to the other invoice to mark it as paid.

Here's how:

1. Go to the + New menu.
2. Choose Receive payment and select the Customer on the field.
3. From the Outstanding Transactions portion of the page, select the open invoice you want to apply the credit. You may also Filter > the date to locate the transaction quickly.
4. Scroll down to the Credits section and then apply the credit.
5. Double-check everything, and once done, hit Save and close.
   

    

Additionally, you may temporarily hold customer payments in the Undeposited Funds account when the amount is not yet in your physical bank. Then, once the money is already in your bank account, you can initiate a deposit in QuickBooks to keep your records accurate. To learn more, check this article: Deposit payments into the Undeposited Funds account in QuickBooks Online.

If you have follow-up concerns about your invoices and their payments, tag me on this thread. I'll be looking forward to assisting you again.