At the moment it is not possible to align the hatch pattern of a material in a family once the family is loaded into a project. For instance is your family has a brick material and brick model hatch you will want to have the hatch aligned to have full size bricks, but the current problem is that when you try to align the hatch in the family, it moves the whole family and the hatch position remains unchanged.
Please make the model hatch pattern of a family editable once loaded into a project.