Here are a few tips that I have learned over the past few seasons. You had a couple of phrases in your post that are almost answering some of your own questions. "First presentation" - your first cast to any fish is always going to have the highest percentage of a hook up. Your odds go down with each additional cast. "Deeper holes where I can not see the fish" - these are very difficult fish to catch. First of all you don't even know what they are doing or if they are even there. "Muddy spots where they are foraging" - this is the most important thing to learn. Focus on sight fishing for actively feeding carp. These are the most "catchable" fish in the stream. Being new to the game I would strongly recommend that you continue to locate feeding fish and sight fish them.
You may need to do some walking and locate some other fish downstream. If they are stacked up in a spillway there are surely other fish downstream. Don't continue to hammer the same fish all the time. They catch onto the game very quickly.
When they are mudding they are rooting up nymphs and crayfish so buggy nymph patterns using picked out dubbing, marabou tails, soft hackle collars. Flies with a good bit of natural movement will usually entice a carp to check it out. Natural colors like brown, olive or rust have worked well for me. Good luck with your carpin'.
