The Night tab on the Options window lets you determine if and when newly created clocks change their colors to indicate night time or day time. You can also apply this setting to all existing clocks.
Enable day / night appearance for new clocks
The clock will always show day colors if this box is not ticked. If it is ticked, you can choose between automatic and manual setting.
Automatic (based on sunrise / sunset)
The automatic setting will get the clock to change colors with local sunrise or sunset respectively based on its geographical location data (see Name tab).
The manual setting allows you to enter a specific time for day or night colors.
You could use the manual settings to indicate office hours for instance. The day and night time values will always be 12 hours apart if the Link check box is ticked. Un-tick this box to change values independently.
The Also apply to all current clocks now command changes all existing desktop clocks to these settings.