Check pictures of other guy's rig. Most will have the rod tips within a foot of the water. If you can't adjust those holders, Driftmaster makes some with a different angle. Main thing is get on the water and fish.
This an important thing that you have pointed out in my opinion. Rod tips should be close to water, this helps prevent wind from blowing line causing bait to lag behind, hindering the ability to accurately know what depth you are fishing.