To achieve the aim of having no one play the same opponents in round 1 as in round 2 (very sensible) you need to have a structure such as this
Round 1 - 6 games of X top 3 progress (X depends on number of applicants)
Round 2 - 3 games of 6 - top 3 progress
Round 3 - 1 game of 9
Key point is that you need to have the same number of games in round 2 as qualifiers per round in round 1.
Would also make sense to create a google doc with the groups / results in it.
Oh and I'm in