Thank you!
You have to use the Skill Manual from your inventory or bind it to a hotkey, then it opens up a menu for increasing the Skill level or its specialisations and other various bonuses. In this menu you will also see how much EXP each upgrade costs.
As for planting crops, you have to have a seed of the plant and either use it from your inventory or bind it to a key on your hotbar. There are two large plots where you can plant them, one is the empty space to the left of your house and the other is the empty space up the stone stairs and to the right of the waterfalls in the same map.