I sell products from my website which creates an invoice number and its own invoice. Customers pay at time of check out. How do I link this to my PPal entry in QBO?

I'm glad you came here, thewoollyrabbit.

You can simply match the transactions from your online banking. I've outlined the instructions on how to do it below:

1. Go to Banking on the left menu.
2. Click the  For Review tab.
3. Select the transaction to expand the view.
4. Select Find match.

Take a look at this article for reference to learn more about matching downloaded transactions in QBO: Download, match, and categorise your bank transactions in QuickBooks Online.

I'm only a couple of clicks away if you have additional questions or any clarifications. Have an awesome day!