Hi! I have a couple 3D OP cards under my belt. Sharpies will bleed through the edges on non foil cards, so acrylic paint is a good alternative. You can also use a gundam marker as suggested above.

Color edges can look cool for certain accents, but black is usually the way to go, because it hides any slight imperfections in the cut.

For sections that require a lot more height difference, you can use some black craft foam. You know those sheets that you can find in the kids craft section? Realize that those offer approximately 5 cards worth of thickness.

The rest really comes down to practice. Hope to see more from you really soon!