The context menu of nodes and the menu 'Edit' contain commands to Raise the Selection and to Lower the Selection. Please note that nodes are drawn on top as long as they stay selected, so the effect is not immediately visible.
Transparent colors can be set using the color chooser dialog (the 'More...' menu entry).
If you're using group nodes, it should work correctly out of the box. If not, please make sure that your nodes are really part of a group and not only placed on the same location. If in doubt, please see the manual for details.