You can create folders to help organize your citations (e.g. by course, by assignment, etc.). If you are using a citation for multiple assignments, you can have the same citation in multiple groups.
Go to Organize > Manage My Groups to create a new group, or edit your existing groups.
Under the Organize menu, you will also find the option to share any of your existing folders with other EndNote Web users. This is especially useful when working in teams as this way everyone can access the same set of citations.