It sounds like you're new to QuickBooks Online. I hope you're enjoying it so far and I'm glad you're getting caught up! I'll help you enter your invoices even though they've already been paid.
There's two ways you can do this. You can either enter each invoice manually and mark them as paid, or you can record them as sales receipts. The difference between an invoice and a sales receipt is that creating an invoice is a two-step process. First you must enter the invoice, then you'll have to mark it as paid by using the "Record Payment" feature. A sales receipt is essentially an invoice and a payment in one transaction.
To find out how to enter an invoice and mark it as 'paid', take a look at this article: How to create an invoice.
To see the steps on making a sales receipt, check out this link: Create and send a sales receipt.
Since these transactions occurred over the last 3 months, you'll want to ensure that the invoice/sales receipt is recorded with the correct date. That's all there is to it. If you have any additional questions, please let me know. I'd be happy to work with you down below in the comments.
Have a great day!
Record the Invoice as well as the Payment - both with the original dates and reference (cheque) numbers.