The layout of 9V track can be tricky, and I am sure there is lots of advice online about what to do and what not to do, ex.
I personally do not know for certain whether different sections of the track will be energized / de-energized by throwing the switches.
Also, I cannot tell whether a particular configuration will result in a short circuit, even temporarily while the switches are being moved, if the pairs of switches (before and after each length of track) are not moved at precisely the same moment.
I would seek out advice online from a LEGO train forum. Someone has probably solved many of these problems already.