As I don't know your animation or video software I can't take you through it step by step BUT the principle is simple.
Make sure you save your animation with a transparent background in your animation software. Save it as an .avi format file this will then be placed on to a second time, line in the right place, in your video editing software. Depending on your video editing software the animation may have to be on track 1 and the other video on track two or it may be the other way round. You will have to find out for your self. In Pinnacle, which is the video editing software that I am use to, the second track always overlays the first track. Just experiment with what you have to see where things need to go.
I am using SwishMax 2 to create animations and MAGIX Movie Edit Pro 14 to create movie. I tried to export animation as avi file with a transparent background. I imported avi file into movie edit software. I tried to put it on the bottom layer and upper layer. But it still has got a black background color.
As I said in the PM I'm not familiar with these programs so I can't take you step by step through them. You could try using the programs help option. Another option, if your video editing software has it, is to use chroma keying. This is when you use a plain colour usually green or blue and tell the software to make everything of that colour transparent.
Remember, everything of the colour you choose will disappear both background and foreground, so you will have to be cleaver with this and not choose a colour that is in the image you want to keep. Again you will have to look at your programs help option to find out how to do it.
Are you 100% certain that SwishMax 2 will allow you to export an animation with either a transparent background or with a matte? I haven't used this software so I can't poiint you in the right direction. You will need to read the inbuilt HELP for it and see if it can export an animation with either. There may be some setting you need to tick when exporting to enable the transparency and it might just be a matter of doing that to solve the problem.
Also in MAGIX Movie Edit Pro 14 you need to check the HELP file to see how it handles files with a transparent background.