I recently had a contractor install a new boiler in my house complete with circ pump, boiler pump and associated manifold plumbing to 5 zones. Upon inspection, the honeywell zone valves were installed backwards (flow going wrong way) and circ pump is on return side of system (sucking water through zones). I have no circulation through any zones at this point. The contractor is frustrated too and is convinced the problem is the zone valves being in backward - I think it's the zone pump sucking - not pushing the water through the zones. My questions: what is it about zone valves that make them directional and what end of the zone should they be on. Also, can the system pump ever be on the return side of things or is this an absolute no no. When this nightmare started I didn't know anything about plumbing - I should have just watched some YouTube and did it myself!

The direction of flow is determined by the configuration of the inside of the valve. With the valves in backwards and the valve is closed, the head pressure will prevent the valve from opening. I think those are spring return valves. The motor drives the stem down to close it and a spring inside opens it.
At this point I wouldn't worry too much about the pump.