How do I apply a transaction to an invoice? Our tranactions come from our bank account into the tranactions screen. Is there a way to apply the payments to an invoice?

If you don't see a choice below the transaction to apply the payment in the bank transactions screen, you will need to receive the payment by going to the invoice or using the "New" button on the upper left side of the screen and complete the action there. 

I appreciate you posting your concern here in the Community, knapiks. I'm here to ensure you can apply the payment to the invoice created in QuickBooks Online (QBO). 

If your Online Banking is connected to QuickBooks and you have an open invoice, you'll want to Match the existing transactions to link them together so you don't get duplicates.

1. Navigate to Transactions, then Bank transactions.
2. Locate a downloaded record. In the Business view, check the Assign to column for matches found. In the Accountant view, check the Category or match column.
3. Click on the downloaded record to see more details. Take note of the Bank details and the amount. 
4. Look at the Suggested matches for potential matching transactions in QuickBooks.
5. Click on the link next to each match for more information. Ensure the Suggested matches have the same amount and the date range is similar to the downloaded transaction. You can also click on Find other matches if the matches aren’t accurate
6. If find the correct match, select it and click Match.

However, if you don't see a match, to apply the payment to the invoice, you'll want to link it through the Receive payment option in QBO to mark the invoice as paid.

Here's how: 

1. Click + New, then Receive payment.
2. Select the customer’s name from the Customer dropdown.
3. Choose the payment method (credit card, debit, PayPal, Venmo, or ACH bank transfer) from the Payment method dropdown.
4. Select the account where the payment goes from the Deposit to dropdown.
5. Enter the payment amount in the Amount received field.
6. In the Outstanding Transactions section, tick the checkbox for the invoice you're recording the payment for.
7. If needed, enter the Reference no. and Memo.
8. Select Save and close.

On top of that, this article can be handy in reconciling your accounts to keep your books balance: Reconcile an account in QuickBooks Online.

I'm still around to help if you need more help with managing invoices in QBO. I'd be glad to extend a helping hand. Take care always