Transiesta Electrode Run
There is a manual available that states (page 111).


  TranSiesta
  defines the Left Electrode to be the first atoms specified in the SR
  .fdf
  file,
  and the Right Electrode to be the last ones.  The transport direction has to be considered
  to be the the third cartesian axis, the
  z
  axis.  The Left Electrode atoms must have smaller
  z
  components than the Right Electrode atoms.  It is also crucial that the atomic positions
  specified at the left (right) EL calculation must be equivalent to the left (right) electrode
  part of the SR setup.  Here, equivalent means that they can be made equal by a simple
  translation  in  space.   It  is  also  possible  to  use  buffer  atoms.


There is more information that I think may address further doubts in the manual as well. I am not very familiar with the program. So, this is as much as I can help you. You could try asking the mailing list, though SIESTA's mailing list does not get many responses to be honest.