Mostly it's best to walk. However, the area is large and sightseeing is sweaty work on a hot day.
By taxi
By taxi
If you are tired, you may wish to get a cab between some of the major tourist spots. This should be cheaper in low season.
For example, 10 TD the driver offered 7, but he was nice and helpful and patient bought me a trip in December 2010 from the museum down to the Amphitheatre, 10 minutes of the driver waiting around, a trip to the Water Cisterns his suggestion, not calculated in the price, a further 5 minutes of the driver waiting around, and a trip down to Tophet.