Moving parts can be done once they are on the layout pane. Hold the part with the left mouse button and drag it into position. The grid size can be selected by pressing the arrow next to the grid size button 10 and choosing a stud spacing from the drop down list. The snapping feature can be disabled by clicking on the button itself.
When moving a group of parts (e.g. a section of track), it is recommended that while moving, you click and hold actual part which you want to connect to the other part. If you click and hold any other part of your selection you may find that it will try to snap to another part of the grid, instead of to the part you want.
Rotating of parts can be done counter clockwise (CCW) 12, and clockwise (CW) 13. Depending on what needs to be rotated you may want to change the angle of the rotation steps. This can be changed using button 11. A setting of 22.5° is ideal for aligning curved track where as 90° is sufficient for most other applications. Once linked to another part, the part you wish to rotate will always keep its link to part next to it. The rotation step size will be what ever amount is required to reestablish a link with the next available connector on the rotating part. For curved track, rotating the part once it has been linked will "flip" it. E.g. a curved piece of track that was going right will now turn left. Any subsequent parts of curved track you add by clicking on it in the parts pane will also turn left until you choose to flip it again. This can also be done by pressing the space bar once the parts are linked.
Aligning parts can be done by snapping the parts to the grid or simply linking them to another part which is already aligned with the grid. The grid size can be chosen through button 10.
Linking parts is done by placing the colored, circular connector, which can be seen when selecting a lone standing part, over the connector of the part you want to link to. Each part category has a different link color (track, road, Duplo etc.). You can only link connectors with the same color. A successful link will be indicated by the connecting points no longer being visible. If the link is not complete a connector will still be visible on one of the Lego parts. You can hide the connection points through the View > Connection Points menu.
You can switch between the various circular connectors of a part by pressing the Enter key (a straight piece of track has 2, a switch has 3 etc.). If you choose to add parts by clicking on them in the parts pane they will automatically be linked to the connector you have selected using the enter key. When dragged, individual parts will rotate automatically so that they connect facing the direction of the part it is being connected too (especially relevant for curved track).
Send to Back and Bring to Front is an important feature, especially if you have different part categories in the same brick layer (e.g. baseplates and track), or if you want to emphasize the use of a bridge (e.g. one track going over another). This functionality is available through buttons 14 and 15 on the toolbar. How far to the front or back the parts are located depends on when they were added. Older parts towards the back, and newer parts towards the front. By using the buttons 14 and 15 or by right clicking on the selected parts you can choose from the context menu whether to bring them forward or send them back.
Moving, Rotating, Aligning and changing the depth works exactly the same way with Parts, Texts and Rulers. Moreover, all these actions can be undone and redone, see the Undo and Redo section for more details.