Before felting, for sure. After felting it would be impossible to get a crochet hook through the fabric. But I have to agree that using a crochet hook sounds like an awful lot of work.
No, there's no special trick to holding eyelash yarn. The lashes should be pretty evenly distributed between the front and back of the piece, but if it's not, I'd suggest using a fine bristle brush and *lightly* brushing the knitted piece on the right side before felting. This technique is also sometimes used when working with a mohair yarn to bring out the halo (or fuzziness). Just brush lightly and don't pull any snags. Good luck!