I have to be honest, we avoid working directly with builders unless the client has no choice.
There are several ways to get the result you want. One I've already mentioned above. You should also set price levels within each item such as retail, discount, and builder as the price level names. This would be useful when you set up a project's Options. After you have entered all of the necessary information to set up your project and before adding any items, go into the project's 'Options' menu and select the 'General' tab. Then change the pricing default for that project to 'builder.' Then all of the items you add to that project will be based on that price level.
To handle the labor side of things, I would use labor SKUs in each package and check the 'Ignore labor calculations on equipment' within the package.
Let me know if this doesn't make sense once you play with it.
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