Hi VjRuby ,
i think you should "render" your clips with alpha channel. Then they are automatic transparent.
Best is to use Quicktime codec "png" with alpha.
here is a tutorial from deepvisual: https://www.youtube.com/watch?v=iDyxDRkjiVc
And there is a new Codec for QT called HAP . This codec is graphic card optimized and is able to hold an alpha channel too.
here is the download: http://www.modul8.us/2013/11/04/hap-codec-v2-available/
here is a thread about codecs: viewtopic.php?f=3&t=8009
i hope this helps you:
there is a manual available which is very helpful because you can work with the software and read at the same time.
well i found this helpful.
you can buy it from "yourspace" where you also can buy the software and hardware