There are two ways the prequel stories can be fit into the trilogy. The first, vastly preferred by the author, is that they be read in order of release. This prevents potential spoilers and allows the prequels to fill in backstory for the trilogy.
The Binding (short story, available free to newsletter subscribers)
At Any Cost (novella, available free to newsletter subscribers)
If the reader prefers to read the stories in chronological order according to story events, they would fall as follows:
At Any Cost
This will not spoil the major plots of any books, and allows the free books to be read first, but may take the surprise out of a few twists and turns along the way.
Finally, the novels might be read first, with the bonus stories added after (again filling in the backstory).