Between the parking lot at Sorrento Valley Blvd. to the parking lot at Black Mountain Rd. There are two main trails that follow the creek. One on the North side, and one on the South. Each trail is a little over 6 miles, so it would be a long day of hiking if you were to do a complete round trip. In addition to the main trails, there are lots of smaller single track trails. There are 5 places where you can usually cross the creek. 6 if you try crossing at the waterfall. Some of the bridges get washed out after heavy rains, so you can’t always count on them.
I would not recommend a road bike on the trails. None of the trails are paved, and parts are pretty rocky. Also note the “rules of the road” which a lot of people ignore. Bikes are not allowed on single track trails, unless marked otherwise (I see riders on them all the time though). Bikes must yield to pedestrians and equestrians (hardly ever see this happen). Pedestrians must yield to equestrians.
Carli mentioned the parking lot on Sorrento Valley Blvd. The other official access point along Calle Cristobal is a narrow hike/bike trail that you can access at the Camino Ruiz Park entrance. This park is at the East end of Calle Cristobal. There are a couple of steep spots along this trail, so be careful but it is awesome.
I’ve biked, hiked, run and geocached in the canyon for over 10 years now and have enjoyed it every time.