There may be more than one way to do this but one way to do it is using Pipelines.
You would have a table of employees and in the table every employee would be a child of a department. There would also be a field indicating the [Status] of the employee as to whether they are Active.
You would also create a Child table on Departments which would be for a new table called Daily Employee Attendance. That Tables will have field for the date, a field for [Present?] (set the default to be checked) and it would be related to the employee table as a child and also be related to the department as a child.
The pipeline would set to be run every day at 1 AM in the morning and search the table of employees (filtering on status = Active) and create records in the Daily Employee Attendance.
So each day the department manager would review the department record and be presented with a report of today's attendance records. Manager with deselect the check box for [Present?] For any absent employees. (I suppose you could also do this with the multiple choice fields with choices of present or absent.)
Do you have all this granular data then is it's easy to run some reports by employee to show their attendance by month or percentages or any kind of calculations you want.