How does a customer send me their payment reference after paying by bank transfer or UPI?

After placing the order, the customer sees a Submit your payment proof form, either on the order confirmation page or later under My Orders in their account, depending on your settings.

They fill in:

• Transaction / UTR reference
• Amount paid (optional)
• a screenshot, if you ask for one
• a Note (optional)

Then they click Submit payment proof. It appears on the order in your admin for you to approve.

For Bank Transfer you choose what's required and where it can be submitted under Payment proof when you configure it. UPI always asks for a reference on both pages.