so the third round seeds can play each other?
Atletico (most probably) won't be seeded.
In case absolutely no surprises happen in round 2, then these
14 teams will pass the 2nd round and go to the 3rd round :
Rangers, Brann, Partizan, Tampere, Rapid Wien, Dinamo Zagreb, Panathinaikos, Basel, Sparta Praha, Dinamo Kyiv, Anderlecht , Wisla Krakow, Fenerbahçe and Aalborg.
In 3rd round
18 teams are waiting :
Liverpool, Arsenal, Juventus, Fiorentina, Barcelona, Atletico Madrid, Marselle, Schalke 04, Vitória Guimaraes, Steaua, Twente, Spartak Moscow, Shakhtar Donetsk, Standard, Slavia Prague, Galatasaray, Olympiacos and Levski.
This way we get 32 teams and UEFA Coeffiecients decide which 16 teams will be holders and which 16 won't.
According to UEFA Coefficients these 16 are holders :
Liverpool, Barcelona, Arsenal, Schalke 04, Juventus, Glasgow Rangers, Marseille, Steaua, Panathinaikos, Basel, Olympiakos, Fenerbahce, Shakhtar Donetsk, Anderlecht, Fiorentina and Spartak Moscow
Juve can't play against the holders but we can get any of the other 16 teams :
Atlético Madrid, Sparta Prague, Dinamo Kiev, Levski, Slavia Prague, Galatasaray, Partizan, Vitória Guimarães, Dinamo Zagreb, Wisla Kraków, Standard, Twente, Aalborg, Brann, Rapid Wien and Tampere.
I remind you, this is only in case no surprises happen in round 2. If only one surprise happens there and one of Rangers, Panathinaicos, Basel, Anderlecht or Fenerbahce are eliminated then Atletico Madrid will be holders and there will be no chance to get them in round 3.