A more detailed description of your typical "workflow" would be helpful, but what you describe is quite possible in FileMaker.
It sounds like you need a system with both purchase orders (for purchasing from vendors) and invoices (for selling to customers). But that's strictly a guess on my part.
You can link both a costs table and a selling price table to a products table in your database. When filling in an order, your invoice line iitems table can link to the selling price table by product ID and by Customer ID to access a previously set price for that product and customer.
The same approach works for a purchase order, but your line items table here would link by vendorID and ProductID.