Hi Marco,
A Sales Order is an agreement for your customer to buy something off of you, which you may or may not currently have. It is generally used in a product-based business. Sales Orders are transactions and do sync between Method and QuickBooks, assuming that they're supported by your version of QuickBooks.
A Work Order is an order for products or services created internally to reflect a request on the part of a customer. Depending on the kind of product or service your business offers, your work order might express a wide variety of information: cost of a product, an hourly rate for service, discounts and taxes, and much more. Work Orders are based off of Activities since they typically involve a time and place that work will be done, and do not sync with QuickBooks as a result (though once you invoice then, the resulting invoice would).
Hope this helps.
- Justin