Chronie fishing is definitely my preferred fishing method. I start lake fishing at ice-off and fish the lakes usually up to Thanksgiving and I always have one chironomid rod out. In the spring and summer it's generally two. Last summer I put in over 60 days on the lake and chronies accounted for close to 90% of my hookups on the lakes I frequent most. There are a few critical things to remember to improve your success rate. First cruise the shoals with your sounder to look for shoals or flat spots. I've found that chronies don't hatch in the same numbers on steeper slopes or rugged bottom structure. Second, as mentioned above, use two anchors and keep them snug enough so your boat doesn't wonder. I like to fish floating lines with leader about 3-5 feet longer than the deepest area I expect to fish. When I fish deeper lakes like Sheridan and Courtney I usually fish with 28-30 foot leaders.
Some guys like to use full sink lines in these situations where you cast out the same length of line as the depth you're fishing and slowly inch it upward. What I don't like about this method is that you're not covering water and if you do retrieve you're taking the fly out of the strike zone which in most cases is a fairly narrow window. Also, if you use this method in water of 12 feet or less there will be fewer fish cruising under your boat because they're likely to be spooked.
I always use indicators on my floating lines. I use the large ones in orange because of the visibility factor. Another reason I use the larger ones is that I find the fish tend to hook up easier because of the resistance created. Fish often set the hook themselves, especially on the rod you're not holding if you use two rods. I like the indicators that pop off themselves when you're playing the fish as opposed to the toothpick type. Sometimes you have to pull them to hand because the loop of line you've pushed into them is too snug to pop them. Be careful when you're fishing with long leaders when you have to do this because the fish might get into one of the anchor ropes. I've lost some big fish this way.
In terms of leaders use fluorcarbon tippet material. It sinks faster and is more difficult to see. I like Froghair and don't usually have to go less than 6X (6.6 lbs). Some people like to tie their tippet to a swivel for the added weight or they use a tiny spit shot to get the fly down quicker. I tie up all my flies with tungsten bead heads so they sink quickly. Besides, when you use two rods I'll always retrieve the other rod first. That will give the other fly tons of time to get down into the zone. Use a mono leader or tie up sections of graduated line out of mono. It's alot cheaper and more supple than fluorcarbon. Leaders that are tied entirely out of fluorcarbon are stiff and won't hang straight down from the indicator making it tougher to judge exactly how deep your fly is.
The only knot I use with chronies is a duncan loop. This knot will insure your fly is always hanging straight down because chronies never swim horizontally. Set your fly about 6 inches from the bottom to start. The best and fastest way to do this is to clamp a pair of forceps to the bottom of the fly and lower it to the bottom. When it touches set your indicator. If there are a million chronies hatching I'll often use one hook size larger or smaller than the naturals so mine doesn't get lost in the mix. Throat pump a fish every hour or so because different chronies will be hatching as the day progresses. Afterall, there are over 2500 different species of chironomids so it's not very often you can use the same one all day. Don't throat check fish under 12-13 inches. It's too hard on the little buggers.
I always retrieve when fishing using a a very slow mend. When you think you're retrieving slow enough slow it up even more. Some days I get more hookups on the rod I'm retrieving and on others its the rod that's drifting freely. Never troll a chironomid but if you're in a float tube you can kick ever so slowly in the area. Sometimes when the lake is like glass without so much as a whisper of wind I'll pull anchors and take an oar stroke every couple of minutes just to keep my lines straight out.
The best time to fish chronies is between 9:00 and 4:00, civilized fishing hours, but during August I've done well much earlier and later than those times. Fish sometimes key on the emergers so have some chronies tied up with hackles.
There's other tips I could tell you but this is already turning into a book. This should definitely get you started. Good luck with it. When you've got the right pattern it can be a fish a cast. There will be times when you won't even get to retrieve a fly the fish hit it so fast. Sometimes I've seriously thought I should put one rod away because it's so crazy, but I don't. Chaos can be fun!