Diagram layout can be controlled in a number of ways. Diagram shapes can be moved (by dragging them with mouse or by keyboard), resized, aligned to the diagram grid. Read Aligning Shapes and Changing Shape Size topics for more information.
Query Builder for SQL Server allows you to layout a diagram automatically or manually. To resize the diagram automatically, just click the Layout Diagram button on the Diagram toolbar.
You can change shape order either by right-clicking them and choosing Bring to Front or Send to Back from the Shape sub menu of the shortcut menu, or by using the corresponding buttons on the Layout toolbar.