If your running them in series, as with the downboy, I'd recommend using protected cells. If you are using unprotected cells, overdischarge is one of the things that you need to watch for. It's also my understanding that you will need to watch for overcharging of one of the cells too. From what I hear, overcharging a li-ion cell can be disastrous.
I also wouldn't wait to see significant dimming. The downboy will continue to regulate as long as the Vin is greater than Vf, which means that a li-ion cell could be killed before the light drops out of regulation.