You use a fan directed at the cold end above the hot end, to prevent heat creeping up the extruder and causing a blockage through expanded filament. This is normally an issue for all-metal hotends and especially when using PLA. If your hotend doesn't have one and you've been printing successfully with PLA, you probably won't need one.
You use a fan directed at the extruded filament to cool it as soon as it's been laid down, to help bridging and overhangs. You'd only use this for PLA. If you have a RAMPS board, the fan gets connected to D9 on the board and is controlled by g code. If you're using Slic3r, take a look at the cooling settings in the filament settings section.
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