How to calculate my shipping cost
How to Bulk Import Product Costs
VIDEO: Product Options/Setup: Edit Product: Unit Cost, Inbound Shipping Cost, & Keywords
VIDEO: Quick Inline Edit & Save for Product Unit Cost & Inbound Shipping Cost
Yes: if you pay for shipping through Amazon then you will find those shipping costs on your Payout Reports only. You will not have to enter this cost into the Product List, which is reserved for costs unknown to Amazon.
If however you have a separate shipping expense unknown to Amazon, say first from your supplier to your own warehouse (prior to using Amazon's shipping services into FBA), you will need to input that separate expense against that ASIN as normal on the Product List or Product Edit form on the Product Dashboard.
Rule of thumb: if Amazon doesn't charge you for it, Amazon doesn't know about it – and neither will HelloProfit – unless you make HelloProfit aware of your separate expenses inside of HelloProfit. Tutorials on how to do so are available above.