The filter should always be placed in the correct direction for the Air flow. Here is why.
1. Placing the filter in backwards may cause the filter to collapse resulting in air flow going around the filter. Many filters have a wire backing to prevent collapsing against the air flow. The filters first job is to prtect the equipment from dust. Air flow around a filter can damage your system.
2. Air flow in the wrong direction of a filter can create a greater resistance causing a strain on your system. This can increase utilities and shorten the life of your system.