Automatic checkout is usually very easy to integrate into your own product. However, when you have multiple products, or a complex way to pre-calculate amount for a payment (in javascript), you can switch to the manual checkout method for greater control.

Rule of thumb: Use Automatic Checkout if you are confused. Manual Checkout is helpful if you are integrating with a Javascript framework, or want more control in the payment process. See our Checkout Docs for more details.