I use unprotected Panasonic 18350 stacked and 18650's as a matter of routine in my VAMO's and I've experienced no problems at all.
As has been explained, the VAMO's will warn you when the battery has low voltage so as not to damage them by dropping the charge too low. The Xtar chargers are intelligent and have thermal sensors to stop overcharging and to stop the batteries cooking off during a charge cycle.
If you do use your 18350's stacked, be careful using atty's like the Innokin iclear's or CE5's,, the higher voltage can overheat and destroy the heads.
I'm also using the same 18650 batteries in my Smok SID's, they have the same protection and warnings as the VAMO's.
I watched a lot of video's on these devices that specifically stated not to use protected batteries before I purchased my kit. It would appear you can use either, but some people have mentioned problems using certain brands of protected batteries. Apologies, I can't remember what brands caused the issues, a Google search may turn up some further info for you.