Generally speaking it is preferred to pump away from the boiler. Are you sure he got the piping right?
From what you describe he effectively has the zones tied together at the hot side of the boiler. When one pump operates it probably is generating enough pressure to push water through the other zone and the pump that is not running.
You could put one pump at the boiler source and use valves controlled by the thermostats on the return side of each zone. To do this you need to have a pressure bypass to control the back pressure on the pump when only one zone is operating. You really should look at the pump curves and determine what pressure/flow is needed. The boiler manufacturer should have data on what kind of flow to run through the boiler. You really shouldn't just stick pumps on without doing the numbers. There also needs to be an expansion tank. This is not a system amenable to just tinkering it together. There is rather a lot more to it. Too high a flow rate will cause noise and possibly errode components. You don't mention how he has the boiler control connected to the rest of the things. High temperature cutoff? Low water protection? Boiler water temp and return water temp. Too low a return temp can damage a boiler.
If you keep the same configuration you need to control the flow in the zones with more than just the pumps. Think of it like you have two hoses outside connected to one of those splitters at the hose bib on the side of the house. Put a sprinkler on each hose. Turn the water on. That is what you have in the heating system.