Try the Spline Modeler instead to make your cut-outs. Just draw your shapes on the cross section & combine as compound. The boolean thing should be used as a last resort from what I've seen. It needs a pretty dense mesh to work with so if you start with the simple geo-shape presets you're starting at a disadvantage. It may work better with the mesh preset shapes but again, the Spline modeler works very well for this.