You can connect multiple client accounts with your WeatherAds account, as long as they are under the same MCC or Business Manager account.
Simply sync your agency-level account with WeatherAds and you can pull in any campaign for weather targeting from any client account associated with your MCC or Business Manager.
If you wish to connect multiple Business Manager/ MCC accounts or multiple standard accounts not managed by a single agency-level account, then you will need to create a unique WeatherAds account for each AdWords or Facebook account you wish to sync up.