Originally Posted by slickwalker
Can someone give me an explanation as to what exactly the docking minimap feature does in each of the options?
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When you have the Blizzard minimap moved into the Carbonite map it will merge the two together. If it is possible to 'fit' the minimap onto the Carbonite map based on position & scale, it will. In the situations where the two maps cannot be aligned the minimap is docked (top left by default). The various options control when and where the map is docked.
As ChaosInc stated above, if you have the auto scaling turned off it is much easier to keep the two maps lined up.