Most sites use a 60% fixed margin for foodservice departments. To use actual margins based on ingredients etc. you have to get all of the costs on each INGREDIENT item corrected. Start by looking at the cost of the items sold in daily recon and identify any problem items. Included is a screenshot below to show items you are selling items for a retail less that your cost, which makes you negative.
You may need to fix past invoices as an example of how to fix items with incorrect costs. Or you may need to adjust retail to account for the cost, if the cost is correct.
I'll set the system to 60% and once you have all items showing realistic costs and/or retail in daily recon - we can change the setting back to the option of using actual SKU for profit.