As a global admin for the Azure Directory that has appropriate permissions to manage an Enterprise application, you can assign users to applications. The only caveat is that the Azure Active Directory must be Azure Active Directory Premium P1 or Premium P2. To assign one or more users to an application directly, browse to the Azure portal as a global admin. We've already done that here as you can see on the screen. From here, open Azure Active Directory, and then select Enterprise applications. 

Select the application that you need to assign. In this case, we're going to assign box. And once it loads here, select users and groups. As you can see, we have no users or groups assigned to our box application yet. To do so, simply click the add user button at the top. And then from the add assignment blade, select users and groups. And then you can see all your users and groups that are available to you. In this case, I'm going to assign both the box users group that I created, and my own specific account to the application. Go ahead and click select. And from here, click assign. At this point, we've assigned our users and groups to the application. After a few moments, the users, and members of the groups that we added, should be able to launch the application that they have been assigned to.