Hi Jeff,
Right now, if you want to create predefined queries in Explorer Online you will need to create the map in Explorer Online first. These will still work in the ArcGIS app, but as you have discovered web maps created from the Map Viewer cannot be opened in Explorer Online.
The custom locator will work in the ArcGIS app as well, but it will have to be set as the top or primary locator in the organization.
[ATTACH=CONFIG]31321[/ATTACH]
The ArcGIS app will only use the top locator for search.
Hope that helps,
Andrew