An alignment module is adapted to determine the relative position of the spout and the cells in the container via processing of image data such that the spout is aligned within a target fill zone of the cells in accordance with a fill sequence or fill plan instructions in which (a) first, the alignment module is adapted to direct the spout to fill the container with the material in a first mode to a first target level that is less than a peak height of the container; (b) second, the fill level estimator is adapted to estimate the number of cells that are below the first target level after directing the spout to fill in the first mode; and (c) third, the alignment module is adapted to direct the spout to fill the container in a second mode to a second target level that is greater than the first target level if less than a threshold number of cells are below the first target level, where the second mode is generally opposite in direction to the relative spout-container movement of the first mode.