A proper configuration of Work Days involves the following steps:
Allowing your organization members to configure their own work days
You can do this from Check-ins > Manage Check-ins > General Settings.
If you want your own team to be able to configure their own working days, you must turn on this option.
Configuring the frequency and days for a check-in
When editing the settings of any of your check-ins, you can configure the frequency and days.
In example, if you have some team members working on weekdays and others on weekends, then enable all the days of the week, then the members can define their own work days to avoid receiving extra notifications.
Specifying that a check-in should consider each users' work days
From the same check-in settings page, you can define whether you want this check-in to consider the Work Days that each user has defined. If you have this disabled, the check-in will just trigger the questions on the days defined by the frequency, however if this is enabled, it will always check that the user is working on that day, if that's the case it will trigger the reminder.
Team members configuring their own work days
Now that you have the previous settings ready, the only missing part is that each user completes the configuration of their own Work Days.
This can be done from the Skill personal preferences page: