I seem to be having an issue with my BOM only referencing the lower level parts rather than the top level assembly. It is doing the same thing even when I have "Indented" selected as well.

The idea here is to create a "nesting" assembly with all pieces needed to be cut from plate. Then create a sketch at the assembly level outlining the nested pieces, and then using the dimensions from the sketch to show the required size of plate for all the pieces in the description of the BOM. 

As you can see in the picture below, the two parts are actually a view of the assembly which the BOM is attached to, yet everything in the BOM is referencing the individual parts and ignoring the top level even when "Indented" is selected.