We generally put the filter in the general area of the irrigation. Obviously that would be after the pump. In other words it would be where the first set of control valves are located. By putting it out there it reduces the chance of debris entering the sytem due to a break in the mainline. Of course there could be another filter at the pumping station, but it would be after the pump.
We would not place the filter before the pump for two reasons. If it fills with debris it would cause the pump to lose its prime. If not properly sealed during maintenance it would allow air to get into the suction line. Neither would be a good thing.
Of course we do filter the suction line with a foot valve. However, this filter is much more course (1/4" or 1/8" holes) than the filter out in the field. We are just keeping out larger debris that could hurt the pump.