Simple, in Modeller (so your layers load in a correct heirarchy), open the layer browser (Modeller/Windows/Layer Browser or Ctrl-F5). Double click a layer with geometry in it and select its parent layer.
In layout, open the scene editor, and simply drag the objects around, the line that appears will indent to illustrate the new parenting.
You can also select a parent from the object properties panel (although this is only good for the selected object/layer and decendants).
You also want to try looking at performing your parenting before you start animating/deforming objects, and ensure you have parent in place set as it makes the whole task somewhat easier.
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