Andrew
I guess you could use FSMETARS to load a different weather partway through a quick combat flight, but I tend to use it like Skylane describes.
The screengrabs are all of FSMETAR weather, using my cloudset.
You'll find that Mission Builders weather controls, although extensive, really don't deliver very believable weather conditions.
I also seem to remember Mission Builder only saves 1(?) cloud deck to the Mission file, no matter how creative you get.
So, doing as Skylane suggests, hand-editing by copying a FreeFlight weather from the cfs2.cfg into the Mission file using Notepad is the only way to go.
I have noticed that keeping FSMETARS running, when checking out range performance for aircraft by flying in freeflight, it will change the weather as you move from one reporting station to another. Pretty cool, but I expect its only me that enjoys such long flights...