There are many ways to perform authentication with Qlik Sense.
Here are a number of different videos you can watch to help you. Because you are using a token based authentication for your app, it's likely that the session api or ticketing api are right for you.
Here are the videos:
Qlik Sense Session API video https://drive.google.com/open?id=0BxBEVQthCb29b3l1ME1SQXpkZkU
Qlik Sense Ticketing API video https://drive.google.com/open?id=0BxBEVQthCb29VGhoNlN6NEpXa1E
If you are using IIS, here is a video for configuring IIS to use these solutions: IISConfigForQPSAPI.mp4 - Google Drive
The following link has a very thorough walk through for integrating qlik sense into a site. Plus, there are specific interactive demos for problems you may face. This helped our team out a lot. Hope this helps.