I had the same dilemma and bought 2x 18350's and 1x 18650. I fancied "small mode" for using out and about, and "long mode" for indoors. However I found the Vamo is a big heavy lump to carry about (even in short mode), and the 800mAh 18350's only last 3-4 hours. I now use a Vision Spinner and an eGo Twist out and about, and the Vamo mainly indoors - mainly in long mode with a 2000mAh battery which lasts all day.
My take on these modern batteries, in layman's terms, is that they can't be allowed to go completely flat like old-school batteries cos it ruins the chemistry in them somehow, and they can then blow up if you try to charge them. Therefore you get protected ones which will "know" that they're getting flat so will stop "working", and keep a low charge in themselves. Unprotected ones don't have this safety protection, so you'd need to know yourself that they're getting low and therefore stop using them. However the Vamo has it's own built-in protection so it will stop the batteries "working" when the voltage gets low anyway. I've read about the odd problem using protected batteries in Vamo's, something about the two safety features sort of not being compatible, but I, and many others, use protected with no problems, and enjoy the extra safety aspect.
The battery code is supposed to be the dimensions. So an 18650 should be 18mm diameter by 65mm length etc. But some of the big capacity 18650's can actually be 70mm long so might not fit in your Vamo. Similarly they could be a mm thicker too.
Lots of folks swear by the Nitecore or Xtar chargers. They have "overcharge" protection, which does what it says on the tin. Especially good if you use unprotected batteries, as the batteries can be unstable if overcharged (in the same/opposite way as if allowed to go flat). But lots of other folks use El-Cheapo chargers and don't have problems.
