Hi there, @WIP2013. I'm here to provide info about the steps provided for linking a deposit to an invoice in QuickBooks Online (QBO).

If those deposits are the actual payment for the invoice, you can follow the steps given by my colleague above to link them. Please browse through this article to know some things you need to check before proceeding: Link a bank deposit to an invoice in QuickBooks Online. 

I also noticed that you posted the same concern here in the Community that my colleague answered. If you haven't notified yet, you can refer to this link for the details: https://quickbooks.intuit.com/learn-support/en-us/other-questions/invoices-accounts-receivable/01/11....

For reference in handling your customer's transactions in QBO, feel free to check this page: Record invoice payments in QuickBooks Online. 

Don't hesitate to leave a reply below if you have any other concerns about recording invoice payments and deposits in QBO. I'm always here ready to lend a hand.