First, to get clouds to follow terrain, I'd make sure the terrain shader is applying colour(a default 'fractal terrain', added from the terrain tab won't), use the colour of the terrain shader for the depth modulator and then positively offset it by pure white(like Martin describes in the tut' you read) by the amount of metres you want the cloud layer to be above the terrain. To get a better visual feedback of the cloud while building it, unplug the density fractal, then your cloud will be built from depth function alone, which you'll later break up with the density fractal.
Make sure there's enough room left within the final depth of the cloud layer to offset it within, otherwise, you'll end up with a cutoff where the cloud top is. To make the cloud layer takes the same shape as the terrain, use a depth modulator value of '0' so you are building the cloud depth from the bottom upwards. A depth value of '0.5' will build out the cloud depth from the centre of the layer outwards, a depth value of '1' will build it from top to bottom(like the inverse of the terrain.
