Hi @eric_engineer,
I hope this message finds you well. The preferred way to do this is through variants. In the document section click Assembly Variants. This feature allows you to make variants of the design with different component placements, values, or attribute sets.
After you click on the command, you'll be brought to a dialog. Click New and name your variant. Now you can control wether a part is placed or not by unchecking it's box under the appropriate variant.
In the design manager you can easily switch between the various variants. When you run the BOM.ulp look at the top left and you can select what variant to produce the BOM for.
Let me know if there's anything else I can do for you.
Best Regards,

Jorge Garcia
Product Support Specialist for Fusion 360 and EAGLE
Kudos are much appreciated if the information I have shared is helpful to you and/or others.
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