I see our FAQ about fields removed the tidbit about fieldkit and only talk about Twixtor now
In theory both should work (setting it or not in AE – there is a slight performance hit if you deinterlace in AE then FieldsKit), however in practice in this case since you want to key, to avoid problems with interpolated values, you might be better to set in AE to NONE, Key interlaced footage then deinterlace with FieldsKit. You will then need to drop comp1 (where you key) into comp2 where you do FK then.
Pierre