Every Company may set a Siege Window. This is the time of day that a Siege phase will take place when defending in a War.
It is very important to set this time to a time that most of the Company's members are available! This time must be set before the War begins, so set it as soon as possible. If you are the Governor of your Company, make efforts to ask your members what time works for them most reliably. If War is declared on you and none of your members are online during your Siege Window, the attackers will be able to take one of your Territories uncontested, even if you've paid for protection.
To set your Company's Siege Window, use the Siege Window tab in the Company screen.