You can overwrite the existing wallpapers on the iPhone/iPad/iPod and replace them with your custom pictures.
As Europa stated, certain things wont work - annoying I know but it's all we've got. Creating a theme with only a wallpaper is another option as well.
You can SSH them into the file system, but if you copy them into the stock photos folders, they won't show up in the camera roll or folders through the Photos app. This is because they have to be assigned a random file name and doing it with that method doesn't achieve that type of cataloging. Instead, it just retains the original file name. Although they'll be accessible through iFile, they won't be accessible through the Photos app so you won't be able to set them as a wallpaper with the stock method (if they are copied to the device via SSH).
One alternative would be to create a theme with a wallpaper. You could then change the wallpaper through iFile rather than with the stock method and you would be able to set any of the wallpapers you transferred via SSH.
New Photo albums that will appear in the stock photos app have to be created on the computer and synced through iTunes. You can, however, use PhotoAlbums+ (Cydia) to create more albums, but it doesn't change anything I said in post #9. It just allows you to move the pictures that are already in your camera roll into new folders. You still won't be able to SSH wallpapers into that folder and set them as a wallpaper with the stock method.