So with all the info about lithium ion battery health do you leave it plugged in over night or do you charge enough to make it through the night them do a full charge in the AM when you can immediately remove it from the charger?
You'll note that even the stock image will boot to a special mode when you plug it in - showing the little liquid battery icon.
Lithium ion batteries are very good at being topped off between feedings and they don't tend towards overcharge issues. The only thing you need to worry about is draining them completely and then letting them sit around for months on end. These batteries have some smarts in them to prevent losing charge completely (they shut off before they completely run out) and to prevent overcharging which is why I never buy knock-off batteries.
I leave it plugged in overnight and haven't had any issues to date.
That's more of a reporting issue than anything else. You can clear the battery stats by rebooting to recovery, but fundamentally battery reporting is a black art. Based on the voltage they're guessing how much charge is left in the battery but the voltage will vary depending on draw and the rate of discharge isn't exactly linear either. In short, battery reporting is more of a rough estimate than anything you should really be too concerned about.
There is also a way to report 1% increments, but there's a good lesson regarding accuracy vs. precision in there