Flaps are deployed to lower the stall speed of the aircraft by increasing the lift coefficient of the wing at the expense of higher drag.

I think you're confusing flaps with air brakes. Flaps are wing extensions that deploy downwards to increase lift and drag, air brakes are panels that deploy upwards to produce lots and lots of drag to slow the plane down after landing, like a parachute.

Flaps are down during landing and take offs (to different extents).