Don't think you can calibrate GPS speed. It is derived from the time the boat takes to move from one GPS derived position on the ground to another. It gives you speed over the ground. The log speed is derived from the movement of the electromechanical impeller through the water. Calibration of this is adjusting the way the software reads the signals from the impeller. The two "speeds" are only the same if the water is static in relation to the ground, that is there is no current moving the water in relation to the ground.
Some argue that speed through the water is of limited use for cruising, but (if it is accurate) it allows you to get a good idea of the strength of the current (if any) that is affecting your boat when compared with the speed over ground. It also helps you judge the impact of sail trimming for example on the performance of the boat.
I largely ignore log speed now on my Garmin, partly because I also have difficulty in calibrating it and partly because the impeller gets easily fouled. My sailing is largely along the coast where tides can be significant, but are very predictable so passage planning concentrates on going with the tide. Speed over the ground (GPS) gives a good measure of progress and I can judge how well the boat is sailing (or motoring) without the log speed through the water.
