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I'm not sure I understand exactly everything you're experiencing, but here's how it's supposed to work.
Your first layer when you open a new blank document will be called "Background". You can either work directly on the background (filling with color or doing brushwork) or paste new papers, pics and elements into the document. Each thing will be placed on its own layer. PSE does that automatically with pasting new things into a document.
You will have troubles sometimes doing things on the background layer (like deleting it) because it is called "background" -- you simply have to rename it by doubleclicking on the word "background" in the layers palette, then you'll have an option to name it layer 0, and either accept that or give it a new name and press OK. Then you can move that layer around like any other layer. Did you realize that you can easily reorder layers by clicking on a layer, and with the mouse button held down, you drag that layer to where you want it and release the mouse button?
Once in awhile, either by accident or because you chose to, a layer can become locked. You'll see a tiny little padlock icon on the right side of that layer's name in the layer palette. To unlock it, click on that layer to make it active, then click on the little padlock icon at the top of the layers palette. You should see the icon disappear off the layer. If you want the layer locked, then you just click on the padlock icon to lock it.
Generally, the background paper is the bottom layer, but not always the "background" layer (I usually end up renaming it to layer 0 in case I want to throw it away or whatever). Then your photo layers, and finally your elements layers. But obviously you might have several layers of background papers and mats, and sometimes you want photos to overlap, say, ribbons so there are no hard and fast rules here. Think of it as building a real paper layout.
There will be times you'll have challenges like wanting several layers to overlap in seemingly impossible ways; that will get you into making duplicate layers and erasing parts of layers to allow parts of other layer to show. But that's maybe a little more advanced than you are right now. Something to look forward to!
HTH and good luck! Post again if you still have probs.
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