When you start ArcGIS Explorer for the first time, the default map is automatically opened for you. The default map is also the starting point for new maps that you create. By default, the default map is the Esri default map, but you can specify your own ArcGIS Explorer map (.nmf) to be the default map for the configuration. Select the Use your own map radio button and then click Choose map... to browse for the nmf you want to use as the map for your configuration.
The default map still opens after making changes to the NMF that the config points to.