I looked in the online manual, but all I am trying to do for example is set (Cube 1) on layer 1 and take (Cube 2) and put that on layer two but I cannot figure out please help thank you!
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Assuming you are talking about the viewport layers you see in the header:

Then just press M with the appropriate objects selected and click on the layer(s) you want them to be visible on.

Another method is to use the properties window, object tab, relations pane; the object will appear in one or more of the layers represented here by activating the button. The relations pane is illustrated in red, and in the image is in the default position.

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1You can also use the keyboard number (not the numpad, but the numbers above QWERTY). For example if you press M2 it will move the selected object to layer two. Pressing M shift 2 will make your object exist in layers one and two. Additionally to navigate between layers just pressign the number will make that layer active. – Sep 28 '14 at 03:21