Do both of your pumps have a filter installed along with them? Water feature pumps will often not have a filter, as they are simply recirculating water to supply the water features and the pump strainer basket is sufficient. However, depending on the type of water feature, sometimes a filter is also installed to keep debris from clogging water features which utilize smaller orifices (sheer descent type). You will want to make sure that the pump with a filter attached does most of the circulating, as this is what filters your water. If both have filters, this won't matter.
If the current system isn't working as you think it should, it might be possible to run a pipe between the two pumps on the suction side so that you can equalize the suction created. It would be best to have a valve installed on this pipe so you can manage the water flow to the two pumps. I can't say that it's designed "wrong", but sometimes a little "tweaking" is involved for more elaborate installations. I'm also assuming that you can run the pumps independent of each other?