How to use cloning effect if the clips are overlapping themselves?
If the character runs in front and then behind the other character then either a depth map or a manually adjusted mask is going to be necessary.  I'm unfortunately an After Effects guy, so I don't know how you would do that in Vegas.  

If nothing else, you might be able to creatively do it by putting one layer of the character running around on top and another layer of the character running around underneath the character that is standing still and then cutting back and forth between them.  

That is of course assuming that the animations have alpha channel support and that Vegas properly interprets the alpha channel.