You can keep your EndNote library organised by creating groups, for example for a particular assignment. You can add references to several groups and you can also delete them from a group. When removing a reference from a group, it remains present in the 'All References' folder.
How do I create a group?
Select 'Groups' from the menu bar at the top
Click on 'Create Groups'. A group is now automatically created on the left-hand side.
Give the group a name.
How do I add references to a group?
Go to the 'All References' folder on the left and select the references you want to add to your new group/group set here.
Then right-click on the selected references and choose 'Add Reference to' and click on the desired group or group set.