Are you talking about when you sew the individual hexes together in topairs, and then the pairs to form the flower?
Because you don't sew through the fabric or card stock.
You just whip-stitch the edges together, grabbing a bit of the fabric of the both hexagons.
I'll bet you were having a tough time. Yikes.
You'll see how easily (and quickly) it will go together now.
(I can't find an appropriate link - figures, huh? - but they're out there for sure.)