Boat fishing involves techniques different from bank fishing. Also, boat fishing is a two-man affair. If you find a compatible boat partner then stick to him like glue. He is worth his weight in gold. With two of you, you can find fish in half the time and eliminate unsuccessful methods much quicker.
On days where fish location is known my boat partner and I have an agreed approach. He starts at the surface, I start at the bottom and we meet in the middle. Then we try somewhere else and start all over again. Until, of course the fish are found. Two heads are better then one by about three, and a boat partner who comes up with an idea when the going's tough is someone to bring sandwiches for.
Drifting in boats is harder to master but out-fishes anchor by about three fish to one. You need a drogue (an underwater parachute). Never anchor in another's drift.
Standing up in boats is out. It is not so much the safety aspect but the fact that you are so obvious to the fish. If you want to scare fish, then by all means stand up. You can even stand on the seats, like I have seen some doing, but if you want to catch fish, and you can catch fish surprisingly close to the boat then keep seated and short-line (casting no more than six or seven yards).
I carry a coarse angler's box for boat fishing since I find most boat seats too uncomfortable for a whole days fishing. There are seats in production to enable you to sit flush with the thwarts. They are great but for the fact that they seat you too high, in position easily seen by trout.
If you do have to fish at anchor then the best anchor point is off the stern. If you anchor off the bow the boat yaws too much for any control. In gentle winds you can anchor side-on, but you should be drifting anyhow.
The debate rages as to which side of the boat is best. Generally boats drift towards the stern, which means that for right-handed anglers, it requires that the boat be set up so that the stern is on the left hand side when the anglers face downwind. Otherwise the right hand man is restricted too much. In this situation the bow man has the best dibble (moving the top dropper such that it scratches the water surface) and the stern man has the best position to cover fish. So under these circumstances I would say that the bow is best for wet fly, muddler, and fishing blind, whereas the stern is best for covering fish, especially with dries.
But, and it is a big but, it all depends on how the fish are running and on how they want the fly. Look at it this way; fish near the surface move upwind (mostly - in slicks and calm conditions they can move down wind) fish also move away from the sun. In addition, fish often require a pulling fly to be moved at an angle to their direction. This can mean that one end of the boat cannot get the appropriate angle. It could be either end.
I personally prefer the bow but only if I have confidence in my partners casting.
There are several sorts of boat partners to avoid; those who insist on standing, noisy ones, competing ones, and those bastards who fish your side of the boat. If the two of you cast at the same time amazing tangles can result. The simple answer is to cast separately. Which sounds easy but when the fish are showing, things can end up pretty hectic. I always have an agreement with boat partners that when on of us wishes to cover a rise at a time when the other is in the process of casting he shouts "covering", at which the man in the mid-cast must stop the cast and get his rod clear.
This system although completely functional gets some friendly abuse when times are hard on one of the anglers. Let me clarify; when one of the angles is catching more fish than the other, the one who is succeeding less well, might attempt to mess up the timing of the one who is succeeding better, by arresting his casts. There may not be a fish there but he will shout covering just the same.
In the same friendly atmosphere false striking can appear. Fly fishing is a thing of confidence. That confidence is so easy to have knocked out of you when your boat partner is catching all the fish. Try and relax and concentrate on your fishing. You will start catching sooner of later.
Incidentally a missed strike can send flies whizzing back towards you. Apart from the danger element and the excitement factor :-), huge tangles can result. Strike sideways, away from the boat.
Boat fishing is great fun, it is a subtle approach, puts you right beside the fish and allows you to share experiences and ideas with friend. Unfortunately there are few excuses for not catching fish, since there is nowhere for them to hide. The only reason for coming in fishless is either bad technique or lack of feeding fish due either to extreme weather conditions, bad water management or chemical influences. It in my experience is usually the angler's technique at fault, occasionally the weather, and hardly ever the management and rarer still the water authorities pumping strange and offensive substances into the lake (but it does happen - and I do wish they would come clean about it).