Hello JJay03
You should be able to use that charger just fine.
I would suggest just build a little external fixture that wires the cells in parallel, and charge them as a single larger capacity cell, this will balance the cells without the need for a balance tap on the setup. your total charge rate should be around 1-2 amps with this setup. Cut the charge rate in half you are charging a single cell at a time for some reason.
Protected cells are very important here as there is no way to see when you have over-discharged a pair of li-ion cells when they are powering a buck regulated LED module.
I really like AWs 17500 cells and have always had remarkable results with them. They seem to actually come in at over over their stated 1100mAH capacity claim in many cases.
you'll find a couple links in my sig line that will help you get up to speed on the use of these cells in various flashlights...
Nobody mentioned this so far so I'll give you a head start here:
A CR123 is around 16.5mm diameter by ~33.5mm long. Also known as a 16340
A 17500 is around 16.8mm diameter by ~50mm long
As it turns out, 2 17500s end to end fill roughly the same space as 3 CR123s.