Yes, when you assign your players to their teams you will be presented with all the teams within your club that the player is eligible for. An example may be adding a player to the first team and the reserve team.
When it comes to registering the player to their league(s), the registrations will go to the respective leagues each team plays in with one click so there is no need to register the player on several occasions.
For more information on assigning players to teams in Whole Game System, click here