In case of already large textures, which are not going to be used very often, you should try to avoid packing them in the same texture (atlas) like all the other small and often used textures.
Why is this? Because many devices will force you to use power of two (POT) sized textures only, and in case of big textures which you want to put together, this might result in a pretty big file with lots of wasted space.
Furthermore if you have 10 levels, each with a different background and you would put all backgrounds in a single texture, then you have no chance of sending just a single background to your GPU. In every level you would have to send the huge texture file with all backgrounds to the GPU, in order to display just one of them. Thus it would waste not only space, but also GPU memory, which is even worse.
For those reasons and because you usually draw your background just once, you can neglect the overhead of the single texture switch. It is not that expensive and if you do it just once per frame (in case of the backgrounds) it won't make a difference.
So in total: seperate the background textures from the rest and make them individual files.