I had a lot of long pieces of old threaded rod, so they are set in the concrete foundation and the timbers are drilled out and mounted over those, with nuts and washers locking them in place. In addition, the timbers are glued down with construction adhesive.
In this shot you can see the trench drain. The old run has a concrete floor, and we hose it down twice a year, so that drain will (I hope) prevent the new section from getting too muddy.