Assuming Customers and Payments are related in some fashion, there's no reason you couldn't record payment information in your cusomters_controller.
$this->Customer->Payment->create()...
There's no rule that says you must use one controller for each model. In fact, that won't work in the vast majority of real-world applications like you're experiencing now.
I normally segregate my controllers by logical functionality groupings rather than trying to pair them up to models. In your case, I would build an accounts_controller (even if I have no accounts table) and put the login, registration, logout, profile editing, etc in that controller.
I find this sort of organization makes the application easier to maintain, and it makes for more logical paths for end users as well.