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Well what printer do you have?
It depends, Bowden is when your fillament isnt driven directly towards your hotend, Example if the Gear pushing the fillament is outside the printer(case)
Direct is when your Gears that drive the fillament is on your Hotend.
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Since you don't know what a bowden setup is, I'll assume you have the standard Prusa i3, which will uses the direct version of the E3D.
The only real difference is that the bowden version has a tapped end to accept the pneumatic fittings. I went with the bowden version just in case I want to upgrade later down the line.