$0 transactions that go through our free checkout process are intentionally included with other sales that you make through our cart, we reserve the "Free Downloads Log" for download links that are generated without any order or transaction -- such as links created by the "Send Free Download Link" feature or the Newsletter/Updates service.
We do normally recommend delivering samples from your own server directly as there are limits on the number of free checkouts/links that we can generate within a day -- there are no limits on paid transactions, only free ones.
That said, if you don't expect a huge amount of demand for your free samples the way you already have things set up is a good way of handling things, and you will be able to pick out the free samples easily in your transaction log by both the $0 total and the "Free Checkout" payment method listed in the log.
