"Check the 2nd box" means : you want to keep your own players (fake teams or created teams) , like Bundesliga, Brasileirao, Chinese League ...
"Don't check the box" means: you keep Konami's players ans rosters
and for these teams , ENG1, ENG2, FRA1, FRA2, ESP1, ESP2, ITA1, ITA2, NED1, POR1...