I like the cloud layer, since it allows for changing clouds, having 3 layers with different scale, speed and direction will result in clouds that randomly change all the time.
The cloud layer works through a normal map plus heightmap in the alpha channel I think, same to terrain normal maps for parallax. Then the cloud layers get overlapped with 2-3 different layers and they will add up and when a certain threshhold is reached the clouds will appear and if it falls below that they will disappear again. The settings can be set in the object inspector, you need to play around with it a bit until you find the right settings.
I never made custom textures for it though, since the default one is quite sufficient, since you just need a bit randomly generated cloud patterns to generate the clouds, the texture is not directly displayed ingame.
I prefer the basic clouds most of the time, since the texture used there is displayed directly and not used for generating the clouds, so you get more control over how it looks, but it will look more flat and the clouds will not morph over time. So just go with the basic clouds, if you are not satisfied or know how to use the cloud layer. Even many modern games today do not use that advanced cloud system, many still even use skyboxes, since it gives the most photorealistic result, but it will be totally static, the basic clouds at least will move.
PS: I used the cloud layer in Uebergame in the level "Pazifik - Watertown at dawn" and "Pazifik - Dee Am islands in rain", most other levels use the basic clouds, so you can check how I did it, if you want.