If somebody pays me through my connected bank account, do I still need to manually record that transaction or will it automatically marry up to the invoice?

Let's see what options do we have here when recording your transactions, userdom.

If your customer paid through QuickBooks Payments, the invoice in QuickBooks Online will be marked as Paid automatically. Thus, it is not necessary to record the invoice payment manually. You can use this link for reference: Take and process payments in QuickBooks Online.

When the payment is cleared from your bank and is downloaded in the Banking page, you can already Match it to the invoice payment in QuickBooks Online. Here's a link that you can use as your guide: Categorise and match online bank transactions in QuickBooks Online.

If your customer paid the invoice via ACH or bank transfer, we'll have two options. We can do either of the following:

• Record the invoice payment manually and match it to the downloaded transaction.
• Wait for the bank transaction to be downloaded in the Banking page. Match it directly to the invoice in QuickBooks Online.

Feel free to get back to us if you have additional queries regarding the details I've mentioned above. Have a great day!