You can use Conga CLM with the Salesforce Lightning Experience and still accomplish the same tasks with the same features. The only thing that changes is how you access the features, and the process for creating an agreement is slightly different. Follow the instructions on this page to get started when you have the Lightning Experience enabled. Beyond a few different steps, the flows for most Conga CLM tasks remain the same. You can also access Contract Management from the Lightning Console. You can use the Lightning Console to Generate, Regenerate, Activate, Amend, Renew, Submit Request, Terminate, Expire, and Clone an agreement.