Problems with different layers in one image? Well, there's no true recipe for this, it's pretty much learning by doing.
But here's some general tips about layer problems:
First, an explanation of layers:
Imagine you had to design a logo. Also, you had some transparencies (the things you write on when you make a presentation

) and on every one of these transparencies you had some part of your logo. For example on the first one you drew the outline, on the second one you drew some letters and on the last one you painted a background. By layering all these transparencies on top of each other, you get your final logo. These transparencies are the layers in Gimp. But in Gimp, you have some features you don't have with real transparencies, for example you can lower the opacity of one layer, making it semi-opaque. But you will find these things out pretty soon

You mostly want to work with layers because if you mess something up really badly while making the background, you dont have to start anew, but instead you can just delete the background layer and redo it without affecting the text or the outline. Or for example if you want to resize your text in your logo, but you don't want to rezise anything else (the border, the texture, anything), it's a lot easier if you have your own text-layer. You just resize the layer, reposition it and everythingelse is untouched.
Also, as a side note, every photo/image/whatever consists of 1 layer. Once you save your XCF files as, for example, JPGs, all the layers are flattened to one single image layer. You cannot edit your single layers after you flattened them to one big image. That's why the "universal save extension" XCF (as you called it

) is always best to use if you didn't yet finish your work and you would like to further edit your image later on.
Back to your problem with resizing and positioning when opening new layers... It's kind of tricky in Gimp, but I'll try to explain:
The first layer you open up in gimp determins the canvas size (the "visible part" of your image). If the first layer is 500x500 pixels, the canvas will have the same size. If you now add a second layer to your first one (for example if you want to add a logo on top of an image and you add your logo-layer to your image) and the second layer is BIGGER than your first one (in pixel dimensions), the canvas itself will not resize, thus giving you a 500x500 "window" of your bigger image. It's easier to explain with images:
1) My first layer, some plasma background layer, 500 by 500 pixels:

Let's say I wanted to use this as a background for my photo-album. Thus, I want to add a photo on top of it. As an example, I'll take some photo I shot in my last Math lecture:
2)

This one is a LOT bigger than my background (it's 4288 by 3216 pixels), scaled down to 12.5% to fit my screen size. If I now open up my image 1), and then I add my second layer on top of it, this comes up:

This is a 500 by 500 pixel window of my big image. I would have to scale the new layer down a lot to fit into my background.
Maybe this didn't quite get your problem, but this is one of the problems some people have when working with layers for the first time.
Anyway, if you have got specific questions about layers, everyone here will be able to help you

Just don't hesitate to ask.
Arzo