I've only had minimal experience with GIMP so I can't say for sure, but if you find it overwhelming that Photoshop may be a little tough too. I've heard the learning curve is not quite as steep as GIMP's, but coming into it with no background at all will still leave you a bit of a climb.
I am pretty sure that GIMP uses layers, just like Photoshop, and a quick google search confirms.
Here's a youtube tutorial for layers in GIMP, which may or may not be any good.
Layers will be the most important thing to understand when it comes to creating custom Dominion cards in any image editing program. When you paint traditionally, you have a canvas. It's usually white and you put colours on top of it. A neat thing about digital image editing is that you can have multiple
transparent canvases all on top of each other. These are layers. By putting different elements on different layers, you can edit some parts of the image without any danger of messing up other parts. You can even toggle a layer's visibility, or automatically add special effects to a layer.
Dominion templates will have several layers. There will be layers for different card backgrounds (e.g. green for Victory cards, orange for Duration cards) where most of the layers are hidden. There will be text layers for the card name, card type, card text, costs. There will be layers with all the extra graphic elements (e.g. the inline coin background for VP shield).
When you make your custom card, you'll choose the appropriate card background and turn on that layer, edit all the relevant text, and maybe make copies of the layers with the graphic elements and move them into place. Then you'll get some card art and drop it in as the bottom layer, behind the card background (which will have a transparent rectangle to let the card art show through).
So yeah, just learn how to use layers and that should get you something like 90% of the way to understanding how to use the Dominion template.