There is a facility built into PHP-eSeller that allows you to set shipping for physical goods. This allows you to set shipping according to the overall shopping cart value. To use this you just activate it in the admin section of PHP-eSeller. The calculations will be applied to the physical items only.
If you do not want to use this facility, you can use the PayPal shipping calculations. In which case the shipping will again be based on the physical items and not the digital items. You may prefer to use the PayPal shipping calculations depending on what you requirements are.