Danno,
When you are bottling (NOT kegging), you need to use the temperature of the beer at the time it is being bottled (usually room temperature, though it might be lower for a lager). The reason is that the uncarbonated beer still has around 1 volume of carbonation in it from the fermentation process, even when sitting open at room temperature.
However, that varies with temperature, so the temperature number is used to calculate the "initial" carbonation volumes so we know how much sugar/additional carbonation is needed to reach your target.
Kegging is the opposite - for kegging use your refrigerator temperature (usually around 41F) to calculate pressure needed assuming you put the kegs in the refrigerator.
Cheers!
Brad