Hi Rebecca,
When uploading in MI Pro all layers in Pro are added to single named map in Spectrum. The named map is added to SSA in its entirety. We do plan to allow admins and end users browse and add individual uploaded layers in a future release. For now admins in Admin Console can enable individual layers to be turned on and off by end users although they will still remain grouped in the legend.
The setting is on the map configs tab and is called "Users can show/hide individual layers "
For SSA 12 all Spectrum layers are placed in a group. Even if one layer is loaded it will be in its own group. The group name is taken from the named map.
Regards
Andy