The alert screen shows the status of the squads at all times, plus enables Civ alerts, once a safe burrow is created. The squad Menu assigns the squads to begin with, to either active or inactive status,and the alert menu also. When you create a new Alert, it opens up a new menu on the scheduling screen, as well as on the squad menu. The alert menu corresponds with the squad menu, visa versa. So when you make a new alert, you can schedule the actions you want your military squads to take during the alert, instead of either active, or inactive schedule. Making a new alert opens up new options for the military to take.
Soooo, you make a new alert, named bugout. Have a burrow that is safe, which contains the levers for drawbridge closing. Create some spots, using notes, where you want certain units to station. Creating the new alert, you have a new schedule page. So you have your archers station at one spot, your melee station at another. To do this, go to each squads schedule for that alert. Copy, paste pertinent orders, same for each month for that squad. So when the gobbos arrive, activate the civ bugout alert, go to the Squad menu, chose a squad, then scroll till bugout appears. Do this for squads you want. They will go to that position, you ordered them to, in the alert schedule. Adding a new alert helps to give the military better options, than active, or inactive. Also more options on the Squad screen, than move, or kill orders