Have you set up Job types (projects) in Quickbooks yet? I think this is the first step. (Lists - Customer & Supplier Profile List - Job Type List) Here you can create your Job types or Projects. When you set up (or Edit) a Customer, in the Job Type tab there is a box to Select the Job Type (amongst other options). When you enter a sales invoice to that particular customer QB automatically allocates the net amount to the Project/Job type you have specified for that Customer.
Conversely when you enter a Purchase invoice there is the option to allocate the invoice to a Customer and to tick whether it is billable or not. If you add it to the Customer with the Job type specified then it adds the net amount of the invoice to that Job/Project.
You can make it a whole lot more complicated than that, but that is the limit of my knowledge unfortunately. Hope that helps a little.
