If you have a business where you primarily are providing customized services and products to your customers, you should have an ERP system that allows you to easily track all costs associated with a job, and allows you to easily invoice your customers for the work.
One way to do that in Dynamics GP is to use the Project Accounting module. The advantage of using the Project Accounting module is that you can track different types of transactions and costs, e.g. timesheet data, purchase orders, inventory items, and miscellaneous transaction types. If you need to break down the job into different tasks to facilitate reporting and management, you can easily do that as well. There is also a flexible billing process that offers a number of different ways to bill for your work, e.g. down payment, per item delivered, % of completion, etc.
This video shows one way to manage job cost operations in Dynamics GP. The Project Accounting module can be used to track costs and profitability for job cost businesses: http://youtu.be/UslfwOvJeic