When you add new encoding settings to Mediasite, you must synchronize them with the ones on the Recorder to use them with your local presentations:
To synchronize encoding settings on the Recorder with ones on the connected Mediasite, click Settings > Presentation Settings > Sync Encoding Settings. Your new encoding settings will be available in the drop-down lists when you add streams in a presentation setting.
Settings tab, Presentation Settings page: Sync Encoding Settings