How does a Payment panel show up in a Sales Order or Ship Doc?

Basically you must first check your QB preferences to make sure that the Integrated Applications, under All Orders and under Properties, have the allow personal information checkbox checked. 

In all orders, select a TERM or create a new TERM and assign it The following are the different types of terms you can setup: 

Accounts Receivable: No payment will be taken in All Orders. All payment will be received in Quickbooks after the order has shipped and been invoiced. ( this will not show the payment panel) 

Full Payment On Order: Orders cannot be filled nor can linked transactions be created until full payment has been taken. 

Full Payment On Shipping:Orders can be filled and quantities allocated but cannot be shipped until full payment is taken. 

Partial Payment On Order, Full Payment On Shipping: A payment must be taken on the order for part of the total amount before it can be filled or creating linked transactions. Payment must be made in full before the items can be shipped. 

Manual Payment Entry:There are no rules for how much of the order has to be paid for but the ability to collect payments will be enabled for orders with this term. 

The last three types will enable the payment in AllOrders you must select the one most convenient to you then on the Sales Order select the TERM you associated with these payment methods