Single Payment allocated to multiple invoices

I'm here to ensure you're able to record customer payments in QuickBooks Online (QBO) accordingly, @ryanl666. This way, you can keep your sales and income transactions updated.

In QuickBooks, payments will only be separated once the invoices are owned by two different customers. With this, you'll have to combine multiple transactions into a single record so QuickBooks matches your real-life bank deposits. Based on your scenario above, you need to receive the invoice payments and make sure to deposit them to the Undeposited Funds account. Then, create a bank deposit to select those two payments. But before doing so, you'll first have to fix and correct the transactions by undoing/deleting the payments you've created. 

Once done, match the deposit to the downloaded bank transactions through the Banking menu. Let me guide you how.

1. Go to the Banking menu.
2. Select the tile for the account you want to review.
3. Go to the For Review tab.
4. Find a downloaded payment with the Match option under the Action column.
5. Note the Date, Description, Payee, and amount spent or received.
6. Select the downloaded transaction to expand the view and review the Matching records found in QuickBooks. 
7. Click the link next to each match to get more details.
8. When it's the correct match, close the open transaction.
9. Select Match.

To learn more about the process above, you can refer to this article: Categorize and match online bank transactions in QuickBooks Online.

After that, you can pull up the Invoices and Received Payments report. With this, you're able to verify that the payments are linked to the appropriate invoices. Just go to the Reports menu, select the said report under the Standard tab's Who owes you section.

Also, I'd recommend reconciling your accounts every month. This way, you're able to detect any possible errors and monitor your business income and expenses accordingly. For the step-by-step guide, you can refer to this article: Reconcile an account in QuickBooks Online.

Let me know if you have other concerns about managing invoices and payment transactions in QBO. I'm just around to help. Take care always.

I have been a QB desktop user forever, recently converted to online and I am pulling my hair out at how inefficient this is.  For example the fact that you cannot quickly find a payment received by our customer and applied to multiple invoices.  If the amount was $ 200 there will be no transaction found.  You literally have to remember what invoice number or amounts they were and search by those individual amounts.  Desktop steps Cntrl F $ 200, $200 will come up as payment and look it even tells you what that payment was applied to invoice # 123 in the amount of XX and invoice # 124 in the amount of XX.  Try doing this online, you can't.  Even reconciliation was such a nightmare customer paid 1 ACH that covered 8 invoices.  I had to find each invoice write the dollar amount and reconcile each of the 8 invoices for that 1 deposit.  How is this ok.