I figure that managing the weather for a gigantic nation like Equestria is no easy task. It's probably a huge operation composed of many teams and departments, and it's mostly government funded. The centre of these operations is Cloudsdale, though Canterlot has some say in the operations as well.
First of all, the Pegasi don't have to control the weather. In Aquellia, for example, the weather is left to its own devices as it is in the Everfree Forest. The clouds do form naturally and move at will. But the Pegasi can control the weather due to ancient magic and have been doing so since the days of the three tribes. It started out that they just pushed the naturally-formed clouds around, but they later developed methods to create the clouds themselves.
Sometimes being a weather pony involves collecting and arranging clouds to form showers, but a lot of the time, it also involves clearing the clouds. Sometimes these clouds were made in Cloudsdale and have just escaped the storerooms, but a lot of the time these are stray natural clouds that have formed and cause problems.
Pegasi have access to magic of their own: the magic that allows them to fly, for example, also affects the weather. They can use this magic to slow or speed up winds, raise and lower the temperature of the air, and cause or prevent thunderstorms, hurricanes and tornados. Because the forces of the weather can be dangerous, there are various levels of teams involved in the management of the weather. At the top, you have the meteorological engineers. These are Pegasi who are highly skilled in weather magic as a result of having a university degree in the study of the creation and formation of meteorological phenomena; both how it works naturally as well as what Pegasi can do to modify these natural behaviours. My OC, Whirligig, dreams of one day becoming a meteorological engineer.
And then you have the various teams beneath them; field weather ponies. A university degree is not required to be a field weather pony, but an apprenticeship is. If the meteorological engineers are the architects and designers of the weather, these guys are the carpenters, electricians and other manual tradesponies who make the weather happen. They are often broken into teams and sent to towns all across Equestria. Each team has a supervisor who makes sure everything runs smoothly, as well as five or six ponies who form the team itself, though the size of the team varies based on demand. Ponyville's weather team is supervised by Rainbow Dash, but there are other Pegasi underneath her who also help out, as seen in look before you sleep and Hurricane Fluttershy. My OC Stormwing is a field weather pony for the town of Trottingham.
Then you have the weather factory and its workers (as well as various levels of management within the factory. Obviously there are going to be some Metorological Engineers overseeing operations here as well, and then department managers and quality control). A lot of Equestria's weather starts life in the factory. Here clouds of all types are made in addition to Rainbows, Snowflakes and electrical systems. There is also a great deal of testing and research done in the factory in close association with the University of Cloudsdale. This research includes the formation and operation of tornados, as well as the containment of storm systems.
In between the factory and the field teams, there are also delivery ponies who work with the factory. These are teams of Pegasi who 'carry' the weather systems created in Cloudsdale to all the towns in Equestria. Clouds are usually corralled and transported that way, with special measures taken when it comes to electrically active clouds. Rainbows are tinned and carried in this manner. When a rainbow is to be used, a field weather pony has only to open the can and pour the liquid rainbow across the sky.
The story of Snowdrop fits in nicely - snow began life in the same way rain did. It wasn't until Snowdrop came along that hoof-made snowflakes were introduced to Equestria. Clouds are made in the usual manner, then infused with hoof-made snowflakes before being sent out to the rest of Equestria.
I'm still trying to work on my wind theories. I've read a few fanfics where there was a tornado creation section in the weather factory, but Hurricane Fluttershy suggests that Tornados can easily be made in the field with a lot of wing power. I'm thinking maybe tornados are made in the factory and then, like rainbows, somehow transported to the rest of Equestria when needed. I don't think they'd be needed often though, except maybe to assist with moving water when ponies aren't keen on breaking records by doing it the old-fashioned way. Obviously the use of more dangerous elements would be heavily monitored.
Cloudsdale itself doesn't have weather systems the same way the rest of Equestria does. They don't have gardens so they don't need precipitation the same way, so they like keeping their clouds in tact (I figure a lot of rain in Cloudsdale would damage the clouds the city is made out of. Cloudsdale does have its own team of weather ponies, but their sole responsibility is keeping the stray clouds out of the city.)
Anyways, I just felt like sharing this. I'm not trying to create lore for the WoE, and I don't expect everypony to agree with me on this, but this system will probably be referenced by OCs in some of my RP posts.