If you sign up for PayPal Website Payments Pro, your store will also be configured for PayPal Express Checkout by default. This means that in your checkout pages buyers will see PayPal as a payment option (PayPal logo and content). Note that PayPal will appear as an option apart from any credit cards or other custom payment options. Yahoo! recommends that you keep this default setting as it offers your buyers the most flexibility in terms of payment options. You can however choose to hide PayPal as a payment option in checkout.
To hide PayPal as a payment option in your checkout pages: