Congrats on getting your new toy.
I usually hold the battery in for about 5 seconds before slowly inhaling - less chance of overheating the herb that way.
Shake her up and go again, and again until the taste tells you that it is depleated.
Because there is little or no VISIBLE vapour you can mistakenly think that you are not getting a hit, but as you found out - 10 mins later ... whammo
No idea about the beeping charger with that one battery, my batteries seem to hold different amounts of "charge" - the little orange glow from the flight box is the only indication of how "charged" they are. Brighter = more charge.
I don't use the tube either - I find it less hassle without it.