The MagSafe charger unit can remain connected after the battery reaches 100%. Unlike older machines which trickled charged the battery when it was full, your Mac is smart enough to know when the charge is complete and will shut it off. The MagSafe continues to provide AC power to the machine.
Here's an excellent article which explains the entire process. LINK
Batteries are not a precise science. There is no way to 100% accurately measure the charge level of a battery. All laptops have some form of systems management controller (SMC) that monitors the battery and tracks trends. When a notebook is new, the SMC needs to learn about how your battery reacts to load. Over time, it will eventually know a bit more about your battery and be able to give you a more accurate reading.
You should also calibrate your battery occasionally if you intend to keep it on AC power most of the time. This article should be required reading for new owners:
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