What you are showing in the screen shot are the search paths Platform Designer uses to look for IP (looking for _hw.tcl and .ipx files) that will appear in the IP Catalog, not the actual folders that will appear in the IP Catalog. The actual placement of how your custom IP/components will appear in the IP Catalog is set by the _hw.tcl file for each component. Look for a line in the _hw.tcl file for one of your custom components:
set_module_property GROUP "User Logic"
and edit the name there. Again, this is specified in the Platform Designer Component Editor on the Component Type tab, the field named "Group", so you can use the Component Editor to adjust this or simply edit the _hw.tcl file.