Over this past year at WY DEQ we have federated our portal and ArcGIS Server Manager, for the most part this has worked out very well, but we had a few issues to work through during the implementation. With this post I want to let you know what we ran into with our implementation. Since, I had never done it before, I was trusting the consultants analyst who performed the federation on their server. We managed everything in server manager before the federation. After we federated, the users and roles are overwritten with users/roles in portal. I should have first taken a screen shot of my users in ArcGIS Server, then I could have quickly added them to portal first. The second item that I ran into was my Secure connection for our map services needed to have the SSL certificate set up in IIS, in ArcGIS Server Manager, and in Portal. Once these were all in place the system started to play nicely again. We only noticed the certificate problems when one of our applications was trying to use a portal generate process. I hope that this helps others with this issue.