You have to pull the opener's cord. Do this only if the door is fully closed. If the garage door opener is released when the door is halfway or even slightly open, its tendency is to slam closed, which may pose a serious danger to anyone near it, as well as the door itself. After disengaging the opener, you can open the door manually.
Yes, you can. Contact your garage door contractor and request for a garage door remote specific for your door's type and brand. Some remotes, when broken, can still be fixed but others no longer function properly so a replacement is always the better option.
The window section can be at the top most portion of the garage door or the one directly below it. The reason for this is that with the window set at a higher slot, better lighting can be promoted.
Garage doors are designed to hang about 4-6 inches in the opening. This allows some of the tension off the garage door cable so that it would not separate from the pulley. If yours is equipped with an electric garage door opener, you can configure it to open completely to provide additional headroom for your car.