Just place three markers on the horizontal (or vertical) surface in the three corners of the rectangle and assign simple coordinates in the Ground Control pane, like (1,0,0), (0,1,0) and (0,0,0). Then press Update button and the coordinate system will be recalculated accordingly.
If you already have some scale-bars applied to the chunk, then you can place markers (without enering their cooridinates), measure the distance between them and change coordinates like (x,0,0), (0,y,0) and (0,0,0).Does it make sense?
To apply new coordinate system you need at least three markers thay do not lay in a single line.