Laying out all the pieces ahead of time will make getting wiring lengths right much easier in the long run.  

The on/off switch is located at one end of the staff, the battery is in the middle (for balance) and the Pro Trinket and battery charger are at the opposite end from the switch. 

If you're using FlowToys caps, remove the insert with a pair of plyers.

Mark the center on your polycarbonate tube.  Align the center of the battery with your mark.  

Measure and cut two lengths of wooden dowel to fill most of the tube on either side of the battery.  Leave enough room on one end for the switch, and on the other end for Pro Trinket.  It's helpful to add labels so you remember which dowel goes on which side. 

Slide everything into your polycarbonate tube and make sure it fits:  Pro Trinket -- shorter dowel -- battery -- longer dowel -- power switch.  You want the power switch flush with one end and the Pro Trinket USB port flush with the other end.  

Take a minute and be sure this is right and everything fits perfectly.