How does the auto apply payments for Customer invoices work? Can you import the payments when you have the customer number but do not have the specific invoice number?

Most payments crm systems will auto generate a sales receipt or most likely an invoice into QuickBooks online.  Only issue I have ever had is to keep an eye on "undeposited funds" and "unapplied payments"

The purpose of the "undeposited funds" is to put payments in to what I would call a "clearing account".  You match payments to deposits in your bank feed.  I find this method helpful in case a card payment does not clear or amount for some unknown reason is incorrect.   If you select to deposit directly into your bank account, depending on how many transactions you have on a monthly basis this could be a mess when doing a bank reconciliation, this is also what I get hired as a bookkeeper to fix quite a bit.  

Hello there, Mauri. Let me add further information about the payment feature in QuickBooks Online (QBO).
 

In QBO, the only auto-apply feature for invoices is for existing credits, which allocates the existing credits match process to open invoices.

Furthermore, directly importing your payments from other systems is not possible. I recommend integrating a third-party app into your QBO to auto-match the invoices with your payments. You can visit our App page to do this:
 

1. Log into your QBO account.
2. At the right panel, select Apps.
3. Click on the Find Apps.
4. In the search bar, enter the app you want to connect.
 

I also suggest utilizing other search engines like Google or Safari to look for the app needed.
 

Alternatively, you can import your bank transactions or deposits into your QBO, match them to your open invoices, and mark the transaction as paid. The following resources will assist you through the process:
 

• Manually upload transactions
• Match online bank transactions
   

Once your transactions are ready, you can start reconciling your QBO account to ensure they match your bank and credit card statements. For additional guidance, refer to this article: Reconcile an account in QuickBooks Online.
 

Comment below if you have any other questions about QBO payments, Mauri. I'll be sure to help you out.