Bill of Materials for Custom Made to Order Goods

We recently upgraded to have Bill of Materials so that we can issue inventory when we manufacture goods. An issue we're having is that Bill of Materials seems completely unsuited to companies who manufacture custom items to order. We manufacture items using large 8ft x 4ft sheets, and usually determine how we use material or leftovers on a per-project basis. So far we've been manually issuing materials used, but now we wan't to use bill of materials so we have a more accurate profit per project (sales order) and accurate COG per project (SO). 

Is there any way to work with Bill of Materials to do this? Can I just assign a BOM to a Sales Order and not to individual products that I then need to make production entries for? Or am I missing something here? Is there another module thats better suited for this? I'd like to say that for SO 006809 we used (2) 8ft x 4ft arcylic sheets, (7) 4ft x 2ft reflectors, etc etc

I'll give an example. Let's say we have an SO that has

(4) 1ft x 3ft Panels

(2) 7ft x 1ft Panels

(1) 2ft x 4ft Panels

And lets say we use (2) 8ft x 4ft arcylic sheets to make these panels. I know that I can allow decimal entries for the amount of material used, but do I really need to manually calculate and distribute the components into the production entries for every SO? If this is the case, BOM is not for us at all. Does anyone have any insight if Work Order is better suited for custom manufacturing?