Of course!
Click on the List button in the toolbar to bring up a list of layers and objects. If you get the outline view, click on the linear list button to get the right view. Now you can just drag objects up and down between layers, just as if you were rearranging them in an outline.
I would highly recommend doing the Tutorial in the OmniGraffle help, and also watching the videos on the OmniGraffle product page at
http://www.omnigroup.com/products/omnigraffle/videos/. I'm not saying that watching them would have given you the answers to all of your questions, but once you have a good feel for how things are done in OmniGraffle, finding your own answers gets easier!