My answers are based on FIFA 08's Manager Mode, taking into account that the 09 mode has not been changed at all...
Yes, if you finish in the top 4, you get to play in the Champions League for the next season. You get to play in the EPL, FA Cup and the Carling Cup in every season.
However, lets say you begin Manager Mode with Manchester United, who qualified for the real life CL in 07/08, you still do NOT get to play in CL for the 07/08 season (ie: the first season) in the game for some reason. I think we can expect the same in FIFA 09.