Near the bottom of the Main Topology Import panel is a checkbox labeled "Auto-Create I/O Flags for dangling nets". This checkbox can only be selected when the Net Names column has been selected (otherwise, the checkbox is disabled). When selected, this option will result in an I/O flag being automatically created for any net that is only defined for a single port (or that is connected only to ports with the same flow direction).
Note: When an I/O flag is created for a net that is only defined on a single port, the routing method for that net will be set to Stubs only (even if the net appearance is otherwise specified in the Net Type column). This greatly increases the clarity of the resulting drawing, since all automatically generated I/O flags will be grouped together in a separate area of the design.
