first off, weather is not really working/ unsupported at this time
that said you can get more than the 3 'easy' options of clear/light/medium,- but you'll need to go into fmb and look for the 'Local Weather' type in Object Properties. you have a choice of 5 types, cumulus, flat overcast, overcast, overcast with breaks and thunder(default),
Place these as you would any other object on the map.
You should see a cloud symbol on the map with a dotted ring around it. By default this will be 1000m radius.
You should also notice the object properties has gained 2 tabs, configuration and properties.
Configuration:- the 3 sections with '1000' in can be altered, 1st is radius in X direction, 2nd is radius in Y direction and the 3rd has to do with height.
Enter whatever figures you find suitable.
there are also 2 tick boxes, rain and dynamic.
Rain doesn't appear to have any rain associated with it. but dynamic can be interesting.
Properties:- the boxes and their labels are messed up so it's hard to tell what is meant to do what but feel free to play around with the sliders- it can only cause a ctd
Thermal intencity seems to be the icing level
Different cloud types have different boxes.
If you look in the .mis file created there are some other variables which you could play with using notepad- you're completely on your own here
This is based on 1.5.... not the alpha patch, which sort of makes clouds a bit redundant as they only draw out a short distance from player.
Good luck, and if you make any discoveries, please report back