The closer the strut is to the bottom of the boat the steeper the angle of attack on the sponsons and looser the front of the boat will run. If you bring it to far up the handling of the boat will become unpredictable and unstable. The reason to raise the strut is that it can make the boat faster because you have less sponson / hull in the water when on full plane. Additionally the increased angle of attack of the hull which exposes more the hull bottom to the oncoming airflow which provides increased lift. Both of these result in the same thing, less water drag.Lowering the strut does the opposite of the above, it will lift the transom out of the water and decrease the hulls / sponson angle of attack. This will result in more hull being in contact with the water and reducing the amount of the hull bottom that is exposed to the airflow, reducing lift. When the water gets a bit rough this is what you are going to want to do.
One way to thing of these adjustments is to imagine the boat as a children's see-saw with the pivot point being the CG, it's easy understand that, when the transom is lowered the bow goes up, reducing the wet area.
Strut angle adjustments
Changing the angle of the strut will effect the direction of the propellers thrust cone. This is another way to fine tune the way your boat is running. The strut has a positive angle when the prop shaft points upwards towards the water surface. In this situation, the transom is pressed down, you will get a large rooster tail and the engine will unload a bit more.
A negative angle occurs when the prop shaft points down, away from the water surface which raises the transom. In this situation, the transom is raised, you will get a smaller rooster tail and the engine will load a bit more. You sometimes need to reduce the angle to allow the boat to get on plane.
Generally a neutral angle is ideal, it only takes a few degrees to significantly adjust the amount of wet area.