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Could you please post screenshots with the pertinent Panels (Toolbar, Layers, Options Bar, …) visible?
You could clipping mask the Smart Object to the rectangle, align it and scale it.
Edit:
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That's what I was lookin for, thank you!
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If you have many images you need to edit thusly you may want to look into automation via Actions or Scripts.
If you want to fill the »empty space« Content-Aware-Fill might help (a but, at least).