"but what about tracking the related freight charges that we pay to send the samples to the folks? Should I enter a Bill"

You enter a bill because you owe for something you don't intend to pay until a later date. Otherwise, you put the charge on the Credit card charge, or a Check entry.

"and use an Item called "Freight" and then assign that cost as a non-billable charge to the final person we are sending the sample to?"

I sure would.