The Input Map functionality is designed to allow you to input an existing map into your BIQ. It is lightly tested.
You'll want to be careful to make sure your resources, units, buildings, etc. on the map match up with those in the BIQ. Unless you are designing several scenarios with the same rule set, this means that you'll almost certainly want to input only blank maps. In the future, support for automatically removing map overlays may be added, but it is not available in the present editor.