In Nopcommerce 3.60, they both are coming in parllel manner , there is way to make it separate?? Mean one in home_page_top and other one at home_page_bottom ??
To edit widget zones where the NivoSlider will be rendered you should edit the source code of the widget. Look at the GetWidgetZones() method in the plugin sources.
If you want place Nivo Slider at bottom please go to nopCommerce_3.60_Source==>Plugins==>Nop.Plugin.Widgets.NivoSlider==>NivoSliderPlugin.cs and change "home_page_top" of method GetWidgetZones() to "home_page_bottom".
I had this "issue" recently which technicaly isnt issue but anyways make sure you go to ContentManagement -> Widgets Then find your widged within list and Activate it !