To move a layer, click and drag on it. You can also move layers using the arrow keys on your keyboard. Hold shift while using the arrow keys to move in 10-unit increments.
There are several ways to resize layers that work in both the canvas overview and the Transition Designer.
Resize a layer using handles
With a layer selected, click and drag on one of the resize handles at the corners of the selection.
Resize a layer while constraining proportions
Hold shift while resizing a layer from its resize handles to maintain it's proportions.
Resize a layer from the center
Hold option while resizing a layer from its resize handles. This can be used in conjunction with the shift modifier to constrain proportions.
Resize a layer using the layer properties inspector
In the Layer Properties Inspector, modify the width and height values. You can also click and drag on the "Width" and "Height" labels.
To rotate a layer, hold command, then click and drag on one of the corner handles of the selected layer. You can also adjust the Z rotation property in the inspector.
To rotate a layer in 3D, adjust the X or Y properties in the inspector.
To flip a layer, click the horizontal or vertical flip buttons in the inspector.
A layer's origin is the point it will be rotated around. A visual indicator of the origin appears when rotating a layer. The origin indicator also serves as a visualization of the current Z rotation angle of the layer. The origin can be modified in the inspector. The origin X and Y values specify the percent of the width or height where the origin should be placed.