I am trying to use a vertical 9:16 video with a 16:9 lens flare overlay, upon exporting I change the settings to an aspect ratio of 9:16 and crop the 16:9 lens flare to fit the 9:16 of the video under and its still exporting as a black bar 16:9/9:16 video. Before exporting, the clips look exactly how I want but after exporting and uploading to youtube its trash. Any tips?
What your before picture shows is vertical video inside of a landscape 16:9 project. What your after picture shows is vertical video inside of a 16:9 project inside of a 9:16 export.
upon exporting I change the settings to an aspect ratio of 9:16
This is your problem. You need to set your aspect ratio before starting the project and compose in that aspect ratio. If you are using Automatic Video Mode, it will only initialize as 9:16 if the first thing you add is 9:16 (and detected as such). You need to create a custom Video Mode in either Settings or New Project before starting the project. The next version will include vertical video modes.