Well as for a charger being smart enough, I'm just using the USB charging cable that came with my device and have it plugged into my computer.. for some reason I'm lead to believe that charger isn't smart at all and wouldn't have that capability unless I'm totally wrong. I'll have a look in purchasing one of those batteries you linked though.
If the chip inside your subox is functioning properly (which it is) and regulating the amperage going into your battery when charging, as well as cutting it off/trickle-charging it when it's full, then it is being "smart". That said, I'm not a fan of internal charging. As @DingerCPA mentions, in a pinch it's probably fine, but all the time/when you have access to an actual charger you should opt for removing them.
In the event that the chip in your Subox decides to stop properly regulating the amperage from the USB charger.. It's gonna be a bad time. I trust any smart charger far more than the on-board charging capabilities of a cheaply-made Chinese PCB. Not knocking them, all my in-use mods are regulated (and all the chips come from China), but it's the nature of the beast. Don't bank on its safety features always being operational.
So now your shopping list is some nice batteries (any one from Illumn that I linked above, RTDVapor is also a great source for authentic cells) and a nice charger. Don't get one of those cheapo 1-bay off-brand guys. Grab yourself a Nitecore i4 or an Efest LUC.