I'm coming in late on this one but.....
If you constantly run your laptop off the battery discharging it continuously it will prematurely shorten it's life. In a few months you'll notice shorter run times before needing a fresh charge. Depending on the type of computer you have, say a desktop replacement, they aren't necessarily meant to run for significant periods of time on battery.
My suggestion is run your laptop off your car's power using an inverter or dc-dc adapter. Use your laptop's battery when the car isn't running.
if you put power into the back of a laptop by what ever means you try, either the manufacturers dc adaptor to a cig socket or via an inverter and laptop psu . it doesnt matter. the laptops power/battery management system will use that power and also charge the laptop battery. in other words it is part of how the laptop is made and unless you modify the power circuits it cant be altered by software alone. the laptop battery wont be used unless external power is removed. you could make a circuit with a relay that is controlled by software and monitors the laptops battery level and then switches to ext power at the point you want . but as stated before the laptop battery isnt going to take a lot of deep discharge cycles ie down to 10% or less too often. i am looking at a dell d620 dual core laptop right now and its battery is 11.1 v and 85 WHrswhich means a capacity of 7600 mA approx. this gives me approx 3 hrs of use. your car battery would probably power the laptop for over 24 hrs straight. then when it gets low you would then have the laptop battery kick in and have 3 hrs to get the main battery recharged.. the laptop battery would act like a UPS.... if your second battery is charged via the car as per normal then you would probably never need the laptop battery. so why do you want to do it the way you said?????
the question would have been more clear if only it was mentioned whether the laptop is going to run as a carputer or just a way of working during the drive to work. in either case, a DC-DC inverter or a car adapter would suffice, wouldn't it? that way, the laptop battery would provide a backup when the car was off. you could even set the laptop to shut down 2 minutes after turning the ignition off.