Have just come across this piece, it was for the play off round last season but assume the 3rd qualifying round takes the same process.
From what I can work out, one seeded team and one unseeded team and drawn and placed into a separate bowl, and then are re-drawn to see who plays home/away. So seeded teams are not guaranteed to be at home second.
http://www.uefa.com/uefaeuropaleague/news/newsid=2130506.html