The weather effects adds up the day it occurs. Therefore if you plant your seeds while it is rainy outside. It gets +2 water, but +0 sun points since there is no sun during rain. If it meets the minimum requirements, the next day it will switch to the next seed stage. Any extra weather points from the previous seed stage will not carry over.
Your watering can is able to water up to +2 water points, but if upgraded can push to a possible +3 water points. For the most part it is completely unnecessary to have +3 water since most crops only need an average of 3 water points per seed stage. Over watering leads to lower quality crops.
For the greenhouse, the outdoor weather does not affect the crops indoors. Sun points would be controlled by how many sunstones you have on the greenhouse.
See crop information for minimum points required for S rank crops.
|Sunny - 3 Sun Points||Clear - 2 Sun Points||Cloudy - 1 Sun Point|
|Drizzle - 1 Water Point||Rainy - 2 Water Points||Snowy - 2 Water Points||Hurricane - 3 Water Points|