You can add an offset after the tween to adjust when the scrolling begins:
controller.addTween('#fly-it', TweenLite.from( $('#fly-it'), 3.25, {css:{left:'2000px'}, ease:Quad.easeInOut}), 0,200);
controller.addTween('#spin-it', TweenMax.from( $('#spin-it'), 3.25, {css:{opacity:0, rotation: 360}, ease:Quad.easeInOut}), 0, -200)
The '0' parameter is the duration of the tween (0 means it autoplays through) and '200'/'-200' are offsets to the default scroll position in which the animation starts.
Also, note that I'm using TweenMax. This is because animations with a duration use the tween progress property, which is only available on TweenMax tweens.