How do you set-up/use an Ultrasound Physical Therapy machine?

Here is the problem with what you have laid out. What you are asking is for information that is going to change with each scenario. There is no cookbook formula that you are going to be able to use. Ultrasound is an exceptionally powerful tool that if it is used incorrectly will cause damage. Knowing when to adjust the dosage is dependent upon multiple factors. The reason for the use of this instrument is to increase the blood flow to an area. While this is happening it can also cause calcium to breakdown thus causing problems for the bone. Remember that the sound waves can bounce off the bone causing pain at the very least and possible burning. So while you say you understand about keeping the sound head moving you have to understand that the sound head has a crystal in it that is vibrating at a specific frequency and it can break if not handled properly. Pulsed waves are used to avoid heating an area. The power that is used is going to depend upon the tissue that you are going through and the result that you are attempting to achieve. So for one person .5 might be appropriate but for another it might be 2. You have to know what you want from the unit.