If the BIQ you open does not contain a custom map, the "Custom Map" checkbox in the upper-right will be available to click. Upon clicking it, you will get a window asking you for a map height, map width, and base terrain for your custom map. The height and width must be at least 16 pixels each, they must be even, and the total number of tiles must be lower than 65,536. The editor will take care of enforcing these limits for you, so you can't create an unusable map.
Once you have a custom map, the Custom Map check box will be permanently checked - you cannot remove custom maps at this time.