Once you merge, you will only be able to use the payment types linked to your Amazon account. If you already have been using Amazon Payments to buy on comiXology, you won't notice anything different.
Paypal is not currently a supported payment method for comixology.com customers for merged accounts. Customers directed to shop on comiXology.fr, comiXology.eu & www.comixology.co.uk will still have access to Paypal if they prefer.
Amazon Gift Cards are still not supported.