You will have a separate pool of points for each Class. Feel free to invest!

The Class and Job share the same points, so if you're a Gladiator and invest points, then the Gladiator's job of Paladin also shares those invested points.

edit: You will not receive points for crafting and gathering classes.

edit: You can reset points using an item if necessary. You will get one of these items when you unlock a job.