I'm not personally familiar with the EB3 but it looks like it allows you to set up three power districts, for example the double-track branch and terminus, inner circuit (with depot/sidings) and outer circuit. That way a short circuit will only stop one section (unless you are unlucky enough to have a train "bridging" across two sections when this happens time). It will also help with fault finding but it might be a good idea to allow smaller sections of your layout to be electrically isolated in order to trace a short circuit. This will involve insulating the rails and creating a means of disconnecting the bus wires, for example a heavy-duty choc-block connector. If your layout consists of several baseboards that can be separated and unplugged then this will be good enough.
Can I also suggest you change your plan to include a left-handed (facing) crossover on the circuit, preferably between the through station and the sidings/depot entrance? Otherwise a train can start at the terminus, run down to the through station and end up in the sidings, but there is then no way to get it onto the outer circuit to return towards the terminus.