I wired a separate fuse box for my IBM R51 in a docking station, monitor, and amplifier. I have never had power issues with my computer, nor had my car battery die from this installation. Nor a fire (keeping fingers crossed). I did not need all the fancy setup offered with a shutdown controller, as I wired a switch from my dash to the docking station.
1. Run a heavy gauge wire from your battery to the new fuse box. Make sure to place an inline fuse as close to the battery as possible. Remember that the fuse rating is related to the thickness of the wire and not the draw from the system. Too much current for a wire may cause it to melt and poof! your car may catch fire.
2. You can now individually fuse each component with the proper sized fuse for the wires to them. I just cut the lighter end off a 120W car adaptor and wired the power for the computer into one fuse slot, the amp into another, the screen into another, and a five volt USB adaptor with spliced USB cable into the correct jack for my soundcard and USB hub, which in turn powers the GPS, mouse, etc. I have never had any power issues.
3. The power to the fuse box can be switched on and off with a relay that is wired to the ignition. That way when the car is off, the power to everything is off, which is how I want it. For some reason, the GPS on the USB hub stays powered from the laptop battery, but in sleep mode, it drains so little, that it very, very, very slowly drains the laptop battery, but not the car battery, as the relay isolates the circuit.
4. Make sure that all your connections are good and solid. Soldered is better than crimped if possible. Also, to reduce any interference, it is a good idea to try to ground everything to the same location with as short a run as possible. The grounds should be equal gauge wire as the power wires. And make sure the ground is clean and solid to a large piece of the car, i.e. frame of well attached body member.