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In this case the eopm has four ports: a0, b0 and c0, c1. a0 and b0 are the optical ports, c0, c1 the electrical ports. They can be at the same location, depending on the specific component. a0 and b0 are the ports that by default are connected to.
If you want to connect an optical waveguide to the eopm, it has to be at b0 (or a0, but that is already connected). You can tell from the color of the stub if the connections match, deep-deep, or shallow-shallow, for the demofab technology. You should have loaded the demofab_klayout_colors.lyp file in klayout for proper visual feedback. Colors are very important in Nazca. See https://nazca-design.org/manage-klayout-technologies for instructions.
After the eopm you indeed have to add a deep to shallow junction and continue with shallow waveguides, or you can just continue with waveguides in the deep cross section, in which case of course there is no need for the transition.