Wrap the neopixels and any other wiring in floral tape.
Arrange the flowers the way you want them, and slip the neopixels inside each one. This is a good time to go back to your code and reorganize the colors of each pixel so it complements its flower.
Wrap floral tape around your battery and feather board, with the switch and antenna coming out the top and the USB port accessible at the bottom.
Add in any additional flowers, leaves, or accents and arrange the fiber optics between the flowers.
Tape the electronics to the flower stems. Finish by weaving the the LED strand through the stems and flowers, and wrap the whole thing in pretty ribbon to cover the floral tape.
To charge the batteries, be sure the bouquet is switched ON, then plug in the USB cable. (It won't charge if it's turned off)
Let them charge completely before the wedding. Overnight is good. Also bring a spare battery for each, and some floral tape and ribbon and pins for emergency repairs. Murphy's Law holds extra power on your wedding day, and you don't want to find that the batteries didn't charge and the whole shebang doesn't work.