Where do you put the gate-protection zener diode in an NMOS H-Bridge?
Yes, they will work fine in those positions (preferably with a small gate resistor). It is the gate-to-source voltage you're trying to limit, so it makes sense to connect the zener directly from the gate to the source.  

You can also use unipolar (or bipolar, as far as protecting the MOSFET goes) TVS diodes instead of zeners.