How can an existing customer become an affiliate? It tells them their email is already in use.

The solution is to simply instruct your customers (or anyone with an existing WordPress user account on your website ) to log in before attempting to fill out the new affiliate registration form.  When logged in, fields such as email and username will already be populated and will display as read-only (non-editable):

Affiliate Area Registration logged in

You can also add a note if a user already has an account on your specific website to the WordPress page that is being used for affiliate registration, either above or below the [affiliate_area] shortcode.