Try fishing early morning (think at or before sunrise) and evenings after the sun is down. That will take care of them seeing the fly line overhead unless your line is bright day glow color. If you are using day glow lines for any spooky trout you may do yourself a favor to either buy a gray or olive line or dye the line you have to olive or gray.
I will not get into the discussion of what fly line is harder for a fish to see here. However, while they all are quite visible when on the surface as viewed by a fish from below, the brightly colored lines are inarguably more visible while casting and especially in sunlight conditions.
As for how to better approach and present your fly, only patience will help you there. Careful observation will show you where the fish are at and from there only a well planned and slow approach will work. Once in position for a 'short & accurate' cast wait a while to be sure you have not been spotted. Many times a fish may see you move to a casting position and once you start waving a rod they are gone.
Practice the 'Bow & Arrow' cast. Pretty simple and in some conditions one of the only ways to make a cast.
If you don't have a 6'6" rod in 3 - 4 - or 5 weight, consider getting one.
Some guys will tell you a 9' rod is great for small streams and tight conditions but I would not fish that way unless I only owned 1 rod. They don't make 6' rods for fishing the Madison River in Montana, but one will work great on the head waters of Grayling Creek there
There are a few things off the top of my head, I spent many a season fishing places like you describe and I use my 6'6" rods here in AK. every year still.