How do you set Credit notes, own set of numbers? So that it does not follow Sales invoices number sequence.

It's nice to see you here today, @tanya6.

Right now, there isn't a way to have your own set of numbers for the credit notes. It's because the system will follow the number sequence on the invoices. I'd suggest manually entering the appropriate number in the Credit Note no. field. View the screenshot below for your visual reference.

I can see how beneficial it is to have your number sequence for the credit notes. Rest assured that I'll take note of your suggestion and submit this to our product engineers. They can find a way to add this functionality to QuickBooks Online (QBO) for future releases.

Also, I recommend visiting this website: QBO Resource Center for ZA. This link provides you more details about our product improvements and free resources for running your business. 

When you want to apply the credit note to an invoice, use the Receive payment feature from the + New menu. Just make sure to choose the customer you selected in the invoice. For the detailed steps, see Step 2 under the Enter and apply a credit note section through this article: Customer Credits Overview. 

I'm just a comment away if there's anything else you need. Take care always, @tanya6.