Since the way to do it from scratch is a bit different than the Xbox way, I'll try to explain it.
Now since the method to put weather in a map depends on the ability to edit the scenario_structure_bsp tag, I am not sure if it can be successfully done in H2V. If the tools we have do allow you to make real time changes to the bsp tag, then proceed as follows....
Firstly, you will need to use the GuerillaTST.exe version of guerilla. It is the only version that shows hidden tag blocks. Depending on the app, Ambiguous may or may not have the entire bsp tag mapped out. Once you open the map in either tool, you will scroll down to this,
Now, next you have to go down the expanded "Cluster" tag and look for this,
You have to manually change all the enum32 (tag pointers), to the weather tag you added to the blank palette at the beginning of the bsp tag. The weather tag MUST match the scenario weather that is defined. Now, depending on how many sub cluster fields the "cluster" tag block has, you can spend anywhere from 10 minutes to a solid hour changing upwards of 50+ tag pointers.
Once you have all the changes made, simply save the bsp file, or if your doing it in realtime, save or sync or whatever the hell it is called.....and the weather should appear! Now this is based on the old tried and true Xbox method, but I know for a fact it works here too, as I can add weather to any map without having to do it thru Sapien. Good luck!