After you open the lid and have taken all of the medication associated with a particular alarm, as indicated by the blue lights on the pillbox, simply close the lid and you're done. The action of opening and closing the pillbox during the alarm window is interpreted as the act of taking your medication. This is apparent upon closing the pillbox, as the blue lights specific to that medication will be cleared. Additionally, the pillbox will log this compliance data, recording that all of the medication for this alarm has been taken successfully.
Another way to indicate that you have taken your medications is through the phone notification. Once you open the notification on your phone, you will be asked if you have "Taken" or "Skipped" your pills. This information will also be logged and saved in the reports section.
If you want to skip rather than take your pills, hold the Ellie icon on the lid town for 3-5 seconds without opening the lid and it will track this as "skipped".