It is really really SIMPLE to edit teams. The system they've used works great I reckon. All you have to do is select a team and then select what player you want to put in that team. Also if a team has had any player losses during the off season (eg Tonga from Parra to Cant), you have to remove him from the Parra team as well.
It is true that if you remove players, it stuffs up the order of the squad, but thats easily fixed. You have to remove all the players, which places them at the bottom of the list of players in the order you removed them. Then you have to put them back in the order you want.
Editing the game makes it so much more fun. I've been tinkering with the squads, and have my predicted 2004 rosters for 4 of the teams. It only took me about 30 minutes.
I LOVE THE GAME now!