What do you mean by "prep?"
When you order from a retailer, they'll ship products that need to be prepared before sending them into Amazon's warehouse. Sometimes things need to be put in bags or packaged more securely. In every case, each unit should be labeled with a special label called an FNSKU. It's like a fingerprint from your Seller account so it doesn't get mixed up with other products at the fulfillment center.
How can I account for prep expenses?
If your prep is cost calculated by the unit (eg. $0.90) or by weight (eg. $0.20/lb), it's as simple as plugging in the value. Everything else is taken care of for you, and you'll see adjusted prices for every product in the Feed.