Make sure it is a good pleated filter and not cheaper grade of filter. As for the upstairs, removing the smaller filters in each register will help with air flow. Also if possible to get a return air register at the ceiling level then it would be better for removing the warmer air rising to the ceiling. Some houses do have them at the ceiling level and some only at the floor level.
If these small changes help then you are all set but if not you may need to call a pro as theduke suggested.
Problems related to residential installations.
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