In Bank Recon it shows receive payment and also a deposit for the same amount and same client? If I accept this it will show twice on the customers account?

Hello userellen-dejong!

You're right. One of the transactions is already a duplicate, so you will need to remove one of them. You can just delete the deposit transaction since the payment is already in your bank register.

To avoid having duplicates next time, here's what you'll want to do.

• If you receive payments to an invoice, open the invoice and click on Receive Payment. Or, match your downloaded transaction to the invoice to apply it as payment.
• On the Receive Payment page, make sure that the Deposit to field is set to Undeposited funds if you won't deposit the actual funds yet.
• When you deposit the actual funds, record it in QuickBooks by creating a bank deposit. Be sure you deposit the payment you created, so it'll be linked to the deposit. 

Check out the video tutorials about invoices and payments for your additional reference.

That's it. If you have other questions in mind, you can always go back to this thread.