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There should be one filter in bottom of unit.Now sometimes installer will choose to put filters in wall grille or install an electronic air cleaner.Do you know if you have either of those?
single filter goes here:
Possibly an electronic air cleaner or filter rack.Do you see a model on the section below the air handler? Can you attach a picture?
OK that is a filter rack, which is an accessory .It is usually installed to allow a better filter than what will fit in the air handler, such as a 4" hepa filter.
You should not have a filter in the actual air handler with this installed.Only the one in the bottom filter rack.