Cut the female connector off the OUT end of your last NeoPixel strand. We'll attach this to the Gemma. Make sure you are cutting the correct connector off! NeoPixels only work in one direction -- you must attach the data wire to the IN end. On most strips, the male connector is on the IN end and the female is on the OUT, but double check your strips to be sure. There is a teeny tiny, very hard-to-see arrow on the back of the strips pointing in the direction of data flow.
Strip the wires about 1/4" with a pair of wire strippers. Twist the wires so they're tidy, then twist the red striped wire securely through the hole marked VOUT. Thread the middle wire through the D1 hole, and the third wire will twist to G.
Solder or bolt on the MIDDLE wire only (for the moment).
Next, find your battery pack and strip the wires about 1/4". Thread the red wire into VOUT and the black wire into G, along with the connector wires.
Finish soldering or bolting the wires to the Gemma. Test by pressing the power switch on the battery pack -- the lights on the face of the Gemma should come on.
Trim any extra fuzzy wires.
If you've already uploaded your code, plug your NeoPixels into the connector and be sure they come on. If they're not coming on, check to be sure the tiny power switch on the face of the Gemma is switched to ON.
That's it for assembly of the electronics. We'll seal up the Gemma with heat shrink and hot glue a bit later, but the next step is to add the lights to the bike and run the animations in place, so you can be 100% sure you like them. A NeoPixel animation can look pretty different once the LEDs are wound around the bike frame, and once the Gemma is sealed we won't be able to update the code. Since we used a connector, we can add lights to the bike and test, then easily remove the Gemma and battery pack to seal it up.