All right, this is simple, but can be complicated at some parts.
First, you create an animation for the caster, so begin the bolt of energy. Then, make the bolt travel to the very top of the window where you make the animation.
Make another animation and call it part 2 or something, begin the bolt at the very bottom of the window, with the same graphic and lead it to the enemy and make the explosion or whatever.
Part 1 should go under the "Caster Animation" and Part 2 should go under "Target Animation" when you make the skill.
Part 1 should logically connect with part 2, so it doesn't look choppy, which is why I said begin with the same graphic.
Do you understand or would you like a picture?