Instance pay during booking feature works like the following example.
Suppose you set instance pay during booking is 50%. That means you must have to pay 50% of your total cost during checkout. You can pay rest 50% after contacting with admin or by hand or later. You can set the no. of percent from global setting panel. You will find this option from here
You can disable this option for the setting tab of main product. Go to the back-end of this product and check the Settings->show/hide tab . You will find this option here.