How to use the LM3880DBV circuit in a multi rail power supply?
Study your block diagram more closely (I've added explicit control lines to make it easier for you): -




  As in the above schematic, it looks like the sequencer has to be
  connected to the end of the last output which is so confusing!


The lower output regulator is permanently activated hence, the voltage it generates is suitable for a supervisory controller like the LM3880. Just because it sits at the bottom of the diagram it doesn't mean it is somehow lower in status.


  While in the LM3880DBV datasheet it seems to be placed before the
  generated outputs


It is - it controls supply 2 to 5 (not 6) via enable inputs. Just study your schematic.