The Shape Builder tool works in a few different ways. To clearly demonstrate it I will clear my artboard by selecting everything and hitting delete.

I will build a simple line art round bottom beaker for this demo. To create this I need 2 elipses (one round, just hold the shift key to make it round) and a rectangle. (Image 1

You will notice the shapes are in wonky spots. It's an easy fix with a perfect result: select all three shapes, click the Object tab, align, horizontal align center. (Image 2)

Select all three shapes, then click the shape builder tool. Click+hold and make a line through all three. release the mouse and viola, done.