Schedules will start at the time you have defined in their settings. This is true even if you have been manually controlling the lights just a minute before. 

Once a schedule has started, any manual control you will do will override it, and the light will not get back to the mode that was scheduled. However, the "end step" you have chosen will still be applied at the specified time.

As an example: you have created a schedule for your kitchen to turn to warm white at 8am, and turn off after 2 hours. At 8am, your kitchen changes to warm white. At 8:35am, you decide to manually change the lights to green. The lights will then remain in green until 10am, when the "end step" is applied and lights turn off.