Hi suggy2014,
http://forum.shipsim.com/index.php/topic,2886.msg28895.html#msg28895
Here you will find a mission editor tutorial. To change the weather place an "area" waypoint and when asked to "define waypoint" choose "Trigger change weather" then decide what you wish to change to. Remember that you must change every thing other than the one you want to "0" or a positive value. If you want it to start raining it's a good idea to change the weather setting to cloudy, as rain does not fall from a clear sky.
Page 19 in the tutorial is the one to look at.
Regards,
Angus.