Purchase the windows you are planning to install. Keep in mind the restrictions a cargo container presents. This means choosing smaller, simple windows as opposed to bay windows. The layout of the container does not allow for certain innovations, though it does have a great deal of flexibility.
Measure the windows you have purchased and then find an accommodating space along the walls of your container. Take a permanent marker and mark the measurements and outline of the proposed window on the wall. This will give you a final opportunity to make changes before committing to cutting the side of the wall.
Using a saw that is strong enough to cut through the thick metal of the container's walls, cut out proposed area for the windows, one at a time. Be careful not to let the metal fall backward once it has been cut, so you do not get injured.
Construct a solid framework to hold the window. Many people choose to use wood to attach to the metal. This will provide insulation and a foundation for your windows. If wider space is needed in order to accommodate a frame and the window, trim more of the wall away with your saw.
Install the windows by placing them within the frames and fastening them. Since the frames are made from wood, your best route will be to nail the windows in tight.