A tip HT gave me when using the cloud editor is to use minus numbers in the "First Create HR:" box. This sets the time that cloud bank is first created to a point before you enter the terrain. That way you do not have to wait for your cloud systems to generate.
I've had no problem with frame rates and clouds either, but then I have a decent PC which runs the alpha at over 80 fps. It is hard for me to know how many clouds to include. I want them to look good but I don't know how much they will affect those players running on marginal systems.
A few things I have found out that may help other terrain builders:
For MA terrains I try to set all the cloud systems to have the same lifetime, exactly one hour in my case. That way the maximum cloud count stays the same however long the terrain runs.
If you put a number of cloud fronts together and you want them to stay together for more than one front life time they will all need to have the same number of rows and clouds per row. This is because even if they are all set to the same speed a front with more clouds takes a little longer to generate on each cycle and so will be a little further away from a smaller front than last time. Over subsequent cycles the group will gradually break up. Again this is mainly an issue for MA terrains.
The density of cloud types in the editor from lightest to heaviest goes something like: 0,1,3,7,6,5,2,9,8,4. So using 0 and 1 in a cloud bank will give lightly scattered puffs of cloud while 8 and 4 will give a heavy overcast. There is about twice as much of the max type of cloud in a bank as the min type.