I just finished editing my video which consists of a Mp4 overlain with a bunch of texts generated from the 3d viewer.
I made each text a separate scene (the texts have animation) and added them using "add" -> "scene" in the VSE. There are four scenes in total. My render output settings are in the image below.
The video looks good while rendering, all of the texts show up and the animations track, however when I looked at my output location there were hundreds of files. It looked like there was one movie file and a bunch of individual frames for the 3D texts.
Not sure how to get them all rendered together. I can send additional information if needed.