It is all done on the league setting page. When you get to the point your ready to move your teams from one league to a combined league, you do this under edit league structure.
For example. if you have two leagues, the NL and the AL and want to move the teams to the NL and make it one league. You click the league options button. Select the NL. Edit league structure to set up the extra divisions, then you choose the al and to the right you will see move team. Click that and move the team to the desired new location. Once all the teams are moved, you can delete the empty AL. Edit names and afffliates to fix up the league name but one warning. If you rename the entire league, it may cause you to lose the previous champions and what not in the league history page, you will stlll have the history, just not the names of the teams that won the league each year.
