It's nice to see you here in the Community, @DogGone. I'm glad to share with you some information and clarifications regarding QuickBooks Payments.
I appreciate you sharing detailed information about your concerns. Let me go ahead and provide answers to your queries.
When you're using QuickBooks Payments, the service combines all of the customer payments (both sales receipts and paid invoices) into a single record each day. You'll learn more about this by visiting this link: Find out when QuickBooks Payments deposits customer payments.
Then, to verify who the payments came from to apply them to the invoices, you need to go to your Merchant Service Center. Here's how:
- Log in to the Merchant Service Center using this link.
- Next, select the Activity & Reports drop-down.
- From there, choose either Transactions or Deposits.

- Then, the list of entries under your chosen category will be shown below.
- Just look at the Name column to see who the payments are from.

For your other concern, you can easily import your bank transactions to QuickBooks Desktop (QBDT) as long as the downloaded file is in .QBO format. Once confirmed, below are the steps to perform:
- In your QBDT company, go to the Banking menu and select Bank Feeds.
- Then, click Import Web Connect Files.
- Next, select the .QBO file you saved and click Open.
- If there's a prompt that asked you to select a bank account, refer to the options below:
- After that, select Continue and then, click OK.
- Once done, go to the Bank Feeds Center to review your transactions.
For reference, please visit this article: Connect with Web Connect (.QBO) files.
Once everything is fine, you're now ready to reconcile your account to ensure they match your real-life bank statement. For the detailed guide, check out this link: Learn the reconcile workflow in QuickBooks.
Please let me know how the steps go. I appreciate any updates you can provide. If you have additional questions regarding QuickBooks Payments, feel free to leave a comment below. I'm always around in the Community to give answers and clarifications. Have a good one and take care.