The mkimage utility combines multiple input image files into a single output image file. It recognizes which of the image files contains the boot image and will place this image at the start. Note that instead of using mkimage, some developers rely on a flash programmer to burn the separate images with appropriate alignment.
For example:
mkimage nto.ifs fs.ifs > flash.ifs
will take the nto.ifs and fs.ifs image files and output them to the flash.ifs file.
If you want more control over how the image files are combined, you can use other utilities, such as: