There is a great deal of finformation in the OptiBPM manual for the creation of multilayer waveguides. Tutorial 10 describes how to make a very complicated electro optic modulator design. You might not need the electrodes, but Tutorial 10 shows how multilayers are created.
There is not likely to be a problem with the creation of the design, the issue is more likely to be related to the limitations of the BP method itself. SiO often has refractive index contrast too large for the Beam Propagation Method. Your simulation might require FDTD. OptiBPM uses much the same interface as OptiFDTD, so if you can specify it in OptiBPM, you can probably do the same in OptiFDTD.