The skillpoints can be earned by level ups ( 5 skillpoints / level ) or win a map and / or convert ressources into skillpoints.
The skillpoints are constant on your play profile and don´t get lost in any way.
Since the newer version you are also able to build a skillmine to gather skillpoints by time on playing a map.
Also you can gather skillpieces to convert them into skillpoints.
1 Skillpoint = 500 Skillpieces
You can use them to buy objects for your protectbase, upgrade for the objects, unlocking new elements on the skillstar, and much more ...
The skillpoints are, beside your level, one of the most important feature you´ll need to use to get progress In-Game.