Are you sure that you can't use the same set of tables, relationships and fields for both?
If you have set this up so that auto-enter settings copy the pricing data from related tables into number fields, you also can simply edit the same fields to enter data for a custom job and with the right relationships, you could, if necessary, prevent values from looking up when you designate the job as "custom" by selecting a value in a field.
Well, I wanted to have 2 different layouts, 1 for an affiliate order and 1 for custom orders, since some fields for affiliate sales are irrelevant for custom sales and vice-versa. But then I run into the issue of the "evaluate this calculation from the context of" layout issue, since there will be two different layouts. Do you have any advice for this?
You can use two different layouts and still use the same fields for your pricing data.
The context of drop down is specific to a Tutorial: What are Table Occurrences?, not a layout so the layout is not a factor in how the calculations evaluate, both layouts can have the same table occurrence.