1. This is My First Time to make a Guide on Steam so it could gone wrong.
2. I'm not good with English, maybe some word or many is not right.

So I'm just gonna say Sorry, and Let's get to the guide.

Skill Box is the item that you can collecting just like the other thing on the island
Skill Box will appear after when you clear The Story quest.
When you collected them, you will get One random skill and it will take sometimes
to reappeared again. Sadly it have Only 2 box on the island and it not guarantee
that you gonna get the skill, sometimes you will get some of a Materials or else.

So you have to collecting items on the island to get a skill too, If you want to get them quicker.

Easy one to get, it close to the Beginning area (But only if you are done with story quest)

This one is close by where you repair a boat.

Like I said, those box will reappeared but it take sometimes
and You have to clear the story quest first before you find it.
So in the meanwhile, Try to collecting item as much as you can
to get a skill and maybe You will get a lot of skill too!

Another Tip : You can use Recycler to get a Skill too.
Good Luck!