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The darks need to be the same settings as the lights, right down to exposure time, but you do not need to shoot the darks at the same time as you are shooting the lights. With a cooled camera you can shoot a library of darks at the various settings you will use for acquiring lights, preferably around 50 of each exposure/gain/temp combination you can use (As Greg posted, best is to use a temperature the cooler can maintain all year) then create a master dark for each scenario (As in 60 seconds -10 degrees, lowest gain, 120 Seconds, 300 seconds etc) which you can then apply to the appropriate lights.
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