Depends on what type of Cloudes you wish to impliment inot your game.
ONe way of getting a nice cloud layer is to have a plain object (flat) that spans the visible world at the desired hieght, now texture this with a nice wispy cloud texture (make sure it has gaps in the texture and parts where there is no cloude) and set its transparencey to the desired level.
Do the same again (maybe have the cloude texture on this one slighty diffrent, wispyer or darker maybe, less or more dence cloud even.)
PLace it at a higher altitude that the one before by about say a in game scale of 100 feet.
Now in game in the main loop make sure the texture on both cloudes is scrolled in the same direction across the plain objects, make the lower ones texture scroll slightly faster that the top one.
And voila you ahve a pritty good looking moving muliy layerd cloude base that moves across the sky with the wind. And when you fly above the first one youll then have cloud below covering in parts the ground and when you look up you have cloud above.
Make sure you use a high quality, detailed texture for best effects.
If you want cloude CLUMPS and is dence cloude objects, well i think thast ushally done in games by useing particles.
another way to do Clumps is to do the same thing as above (2 plaine objects with dencer clumpy coude textures) but make then allot smaller (the size of the cloude) and cros them at 90 degs with each other. Whern the plain objects are make transucent it will look rather nice.