Good question! At this time, if you want certain sites you created to be billed to certain clients of yours, the best thing to do is have your customers create their own Netlify accounts so they can pay those bills directly.
We can help you transfer sites to these different accounts after they are set up.
That being said, if you want to bill your clients instead, the pricing breakdown by site is available on the Billing tab in the Netlify UI. It should be easy enough to identify which sites generate which charges straight from there. If you have specific questions about charges on that page please let us know.