Lunches or breaks can be added to shifts when they are first created or at any time. Once you have added this information into a schedule week it will be there when you Import the shifts into future schedules. This information is added in the shift description field for each shift and then the shift "Paid Hours" can be manually set to account for any unpaid lunch or break time.

So for example if you have an 7:30am to 5:15pm shift with an unpaid 1 hr, 45 min lunch you can enter those begin and end times and then enter paid hours of "8" and then in the shift description you could enter "Lunch at 12."  The break times can then be displayed on the schedules for both employees and managers to see.

You can quickly add this information to multiple shifts using the Multi-Shift Edit schedule view. 

Note: Using this method WhenToWork does NOT allow you to graphically see and account for break time within the shifts. If you need to have accurate worker counts at all times you could in the example above create one shift from 8am-12pm and another shift from 1:15 to 5. This would allow you to have accurate counts on the Availability/Coverage view but then might be awkward if employees use the tradeboard and need to post two shifts to try to get rid of one day's work.