Hi Jess,
Thank you for reaching out on this and WELCOME to the QuickBooks Online family!
The transfer function in QBO is to record transfers between 2 bank accounts or cash and cash equivalent accounts. If you were trying to receive payments for existing invoices, all you need to do is to open the invoice and click on receive payment. Please make sure you are choosing the right bank account the fund has gone into.
Hope this helps, and please let us know if you have any questions. Thank you.