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Location of the filters with respect to the fan shouldn't matter as long as there is no air leakage before the filters. I would let physical constraints and ease of design/use dictate where you put the filters. I assuming you will be installing both a HEPA and Activated Carbon Filters inline with the fans.

Did you have enough enclosure leakage for the makeup air or did you end up cutting a few holes?

Finally take a look at airflow over the heated bed. Some materials like ABS require high bed temperatures as well are high ambient temperatures to minimize thermal contraction. This is probably not a issue for PLA or PTEG but will be for most other materials.