Just drop you a quick line how to assign Enterprise Mobility Suite licenses to end-users. This is is a straight forward process with an one-stop-shop!
1. Sign into the Azure Management Portal as the global administrator of the directory you wish to customize.
2. Click on Active Directory, and then select the directory where you want to assign licenses.
3. Select the Licenses tab, select Enterprise Mobility Suite, and then click Assign.
4. In the dialog box, select the users you want to assign licenses to, and then click the check mark icon to save the changes.
5. Validate if the assignment process was completed succesfully.
When you’re opening the Microsoft Intune Account Portal and retrieves the information of the particular user you’ll notice all components of the Enterprise Mobility Suite are assigned to the user…just by a signle click from the Azure Management Portal.
If you want to automate this process you can use some PowerShell magic and automaticaly assign licenses to end-users. See How to Use PowerShell to Automatically Assign Licenses to Your Office 365 Users how to automate.