I’ve been messing around with Synfig for a bit and I’ve made myself an animation. when rendering and exporting it with the default settings, I am left with a gray background, which won’t go well with the video that I am making. I tried to [render as a PNG sequence and then use blender to put it together, but that just doesn’t seem like a good workflow. I also tried enabling “extract alpha” but that leaves me with two videos which is inconvenient, especially since I don’t know how to use a transparency mask in my video editor (VSDC). If anybody can help me with this, that would be appreciated.
You’re stuck with exporting as PNGs for now as there’s currently no option for video with ALPHA
What (free/open) video codecs do support video with transparency?
The HAP video codecs support transparency though the codec is mostly use in live performances (e.g. vjing, live video manipulation).
It is also possible to use ffmpeg to produce a transparent video as described here Produce QuickTime compatible mov file with transparent background from png using ffmpeg - Ask Different
Both options rely on the media play or video editor supporting those codecs/codec options and not all do.
Here is an example of usage of the 2 videos (color + alpha) using Blender
But in your specific case, you must import your 2 videos in VSDC and compose them with blending modes.
It is like in Synfig, but with videos 
