Long story short - you wanna to export video file or frame sequention with alpha channel (transparency) - is that correct.
If that is the case to do that you should use a file format/codec that support alpha channel. To do that you have to:
1. Go to export settings
2. Chose format Quick Time, AVI or frame sequence f.eg. tiff or png
3. If you chose avi or mov you chave to chose codec that support transparency:
- for AVI - lagarith(free and quite good), or without compression (huge file size) or other
- for QT - Animation, uncompressed, or other third party like DNxHD, DXV - but those two are lossy so not the best for intermediate file
4. Most impoortant: In Channels chose RGB + Alpha - if you can't do that it means that you have chosen codec that doesn't support aplha channel.
Thank you so much for your help!
Very good introductions!