Typically, the POS is used for cash and carry type items or items a customer comes into the store and walks out with. The POS is also used for layaways.
A sales order (which becomes an invoice once the order is filled) is used for items that are not in the store. This could be for a special order, a pre- order, for an item coming in on a Purchase Order, or maybe to place an order for an item that is another retail location. A sales order is also used for internet orders when Springboard Retail is integrated with your e-commerce solution.