The first thing you'll want to do after you open up the template is zoom out a little, because the dimensions are large and hard to navigate through.
Then, find the control which lets you create new layers and create a new, empty/transparent layer. You'll see it added to the Layer tab of your program. Since we're going to be using this layer as a background, you should drag the layer all the way to the bottom underneath all the other layers, so the above layers are imposed on top of the background instead of being obscured by it.
Then, hide the other layers, so only the new, empty one can be worked with. In Pixelmator, a checkbox lets you hide layers, in Photoshop it's an 'eye' icon. Now, you need to create a background.
When it comes to backgrounds, you have a few options. You can create a nice smooth gradient with the Gradient tool, or you can paste in a high-res picture, or paste in some nice, pre-made backgrounds. The picture with the orange background was created with the gradient tool. The other picture with the soft, huey background came from this link
If you're pasting in an image as a background, look for an option that lets you paste it as a New Layer, that'll save you a lot of fuss in resizing the layer to your picture size. You can then resize the layer itself to meet the requirements of the Channel Art.
Lastly, the template comes with a layer called 'Your Art here'. Feel free to delete that, or replace your background image into that layer if you wish to keep it, it's up to you.