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There are two different strands to qualification.
First is Access. This means that regardless of what clubs are involved a countries qualifiers are automatically assigned to certain rounds. In some cases that might mean that one team enters at the first round, and one team enters at the second round. Which qualifiers from each country go into which round is based on performance in the qualifying season. For the Europa league the order is Cup winners, 2nd in league, 3rd in league. If the cup winners are the league champions the order is 2nd in league, 3rd in league, cup runners up. If the cup runners up finish in 2nd or 3rd in the league the order is 2nd in league, 3rd in league, 4th in league (In our case Pats, Derry, Sligo)
When each team is assigned to each round, only then individual rankings come into it. In this case Derry will be a higher seed than Sligo, because of their results in the UEFA Cup a few years ago. Pats and Derry should have the same ranking. All LOI clubs have a higher seeding than clubs in the North. When we played Odense in 2007 they were the top seeds in our round despite being the last Danish qualifier. They were also the top seed in the next round due to their high individual rankings