You can leave it plugged in while the laptop is on, which is also what I wrote. 😛
Just to be perfectly clear, it's okay to leave the charger in over night when the laptop is ON.
Just don't turn it off and leave it plugged in as the battery will then start charging again when it has dropped 1-5% charge.
I'm not familiar with the program, but reading some of his blog, he seems to know what he's doing and has a good deal of battery experience and knowledge. I'd say it's probably a good program to have, if you want a good idea of your battery's cycles, while getting some easy shortcuts to turn off unnecessary graphical windows animation(s) and effects(Windows Aero) and power-control plans.