1. Having it as an open window can lag your PC due to the frame rate going towards the Idle runner and whatever else you may be doing. So leave it as a tabbed-out window
(Although you'll have to start the run again manually)
2. If you spam-click where the fruit icons sit, they'll all activate, it will take a second to register what you're clicking but will work.
3. The apple will only take effect whilst you have stamina, the apple boost is just a 20-second timer in which you have double speed
(No stamina = No effect can be used)
Hope that answers your questions!!