This is going to be a quick guide to recording CSE sequences and converting them to a use able format for video editing. I had a bit of difficulty finding this info at first and I don't think it's on this site so I'll write it up here.
So the CSE can render out frame by frame whatever you have in your viewport. This includes decorators, so turn them off by pressing J or Render->Show Helpers->Show Decorators.
Now would be a good time to make sure your settings are all on Extreme (file->preferences->video) and to make sure shadows are rendered (Render->Lighting->Show Shadows). Since it's rendering frame by frame, it doesn't matter if your computer can't handle those settings.
Next, you want to set your viewport size to whatever resolution you need your final product to be. View->Viewport Size->Custom
For this example I'll use 1920x1080. Don't worry if the viewport overlaps or is clipped, as long as you don't drag any of the viewport sizing it will record to the right resolution.
Now you want to hit the record button (alt+f11). Make sure the checkbox is marked for compression because otherwise you can't name the file (don't know why). Chose where you want to save it, choose the file name, then uncheck the box.
Wait forever and a half depending on the length of your video. 90 seconds took me at least 25 minutes.
The output will be a .y4m video file, an audio output of any sounds you added, and a text document. I've found that I can watch the .y4m file in VLC but not in any other viewer or video editing program. That's an issue. Luckily someone at blizzard (link above) posted the fix.
I'll upload the files you need to convert the video without hassle. If you want to tweak the settings, open the .bat file in notepad and tweak. Mine is set to output to .mp4 at 60 fps in 1080.
To convert, keep both files in the same folder and drag the video you want to convert onto Movie Converter.bat. This replaces the original file.