New LI-ion cells take a few charge/discharge cycles to get "broken in". After that, they'll work fine. The charge life on your 490's seems just a tad light, but a lot of that depends on how much your vaping, the resistance of your coil, environmental temperature during use, etc, etc.
They do not need to be completely dead before charging. In fact, it's not a good idea to ever completely discharge them. The Provari does a real nice job of letting you know when it's time to charge, but I like to charge mine before the button starts flashing.
Unlike the old ni-cad style rechargables, LI-ion does not develop a charge "memory". I've found that a regular use/charge regimen will make the batteries perform better!
I'd highly recommend reading these two articles if you haven't already:
http://www.e-cigarette-forum.com/fo...eeper-understanding-mod-batteries-part-i.html
http://www.e-cigarette-forum.com/fo...eper-understanding-mod-batteries-part-ii.html