As like the fishing information I thought I would make a note of where to find certain mining cave areas and such for myself (and others) and links to the sites with more information as well)
Go to the Smokefinger and buy the Sunpoint Plasma Drill
Equip to a gear slot
Best place to do mining is in caves, but you can find them in open world. You will wanna bring out the drill and listen for the beeps (you can also note on the right side that when your close to one that you can see the distance from one that you are). If you do have issues seeing the blue dots you have to hit you can hit the middle mouse button to zoom in.
Blue deposits are for gems. Red deposits are for ores.
Caves that contain toroids
First map (and legend) is from this site Here
Second map is Here