I assume that this question is in reference to SaaS Applications? 

FlexNet Manager has integration for Microsoft Office 365, but to track license entitlements, consumption and usage for other SaaS Applications, you should check out the complimentary Flexera SaaS Manager solution, which is designed for SaaS.

FlexNet Manager is primarily focused on your On-Premises software (that is installed locally on your desktops, laptops and servers)