How do I get orbs?
Solution 1:
You will discover orbs later in the game. They become more apparent towards the early mid-game. Orbs will spawn in pre-set locations, and can be either found through normal digging, hidden areas, or most commonly found in dungeons.
You may also get the feeling that there are not enough orbs. That is not really true. I remember holding on to my orbs during the early stages of the game thinking there weren't enough to use on all the upgrades.
Turns out, by endgame, you will most likely have a surplus of orbs you won't need. So don't worry about orbs; later in the game (I think 2nd or 3rd dungeon) they'll introduce you to orbs and how they work.
Here's a pic from the Wii version (note, the 3DS version will look close to similar, with slightly "worsened" graphics)
Solution 2:
If you are looking to find orbs right away, here is where you can find your first set. NOTE: This is a spoiler for anyone interested in the question but want to find them on your own.
About 43m down you will find your first "unmarked" cave. It's the one with a long pool of water. You'll need to acquire the sprint shoes from the first cave (marked I) to get it. There is a single square above the pool. Take a running jump from the entrance, hit the top and immediately jump again. Just above where you land you will see the orb in the rocks above you.