Why does Edius divide my clips up into two separate files?
When I drag clips from my timeline to a bin, the clips show up as two separate files, audio and video. What is going on?

This happens to editors who have set up their project to emulate other popular editing programs with separate audio and video tracks, (ie 1V, 2V, 3V, etc and 1A, 2A, 3A, etc). While Canopus was trying to accommodate editors who are used to working with separate Audio and Video tracks, and have made Edius very flexible, there are a few oversights like this and some things just don't work quite like they should. Here is what is happening.
In most editing apps, when you drop a clip on the timeline, the audio portion of a clip will be "linked" to the video so that as you move them or trim them they will always stay in sync. If you do want to move or trim audio separate from video, most apps have a way to "unlink" audio from the video. However, in Edius, if you set up your editing environment with separate audio and video tracks, Edius considers video clips on this kind of timeline to be, by default, automatically "unlinked". By the very fact that you have set up the system to have separate audio and video tracks, Edius believes, for some unknown reason, that you want to have your video land on the timeline, unlinked from its audio.
To the first time user, it may seem like the audio is still linked to the video. It looks, acts and feels like it is still linked. You can grab a clip by the video portion and the corresponding audio portion will highlight and will move or trim together as though they are still "linked". However, if you right-click on the clip you will notice that "link" and "unlink" are not even an option with this kind of timeline setup. They have been grayed out.

And even though your clip may seem as though it is linked, it is not, and that is why it ends up in the bin as two separate files.
What Edius does to make it seem like the clip is still "linked" on this kind of timeline, is to make the files automatically "grouped". In other words, behind the scenes, Edius is unlinking the video from the audio, making them two separate files, but then grouping them back together so they will act as one file on the timeline. Many first time users who set up their timeline to have separated audio and video tracks will complain that they are not able to "unlink" their video from their audio when they want to perform separate trimming functions, that the unlink feature is grayed out. What you need to select instead is "Remove Group" by right clicking on the clip.

To get back to the question at hand, a dragged clip from the timeline creating separated files in the bin seems to be a weakness of the current version of Edius. The bin is just not "smart" enough to know that individual clips that are placed on a timeline with separated A and V, that have never been "ungrouped" are in essence still "linked" and should be represented as one file in the bin.
The only work around I have found is to double click on a clip so that it pops up in the play monitor, and then drag it from the play monitor to the bin. Hopefully the bins in E6.0 will be a little "smarter" and recognize that a clip that has never been "ungrouped" is still, in essence, "linked"!
Something else that should be noted here is that the "remove group" and "set group" functions are not just for use as described above. It also acts as a way to group multiple clips together so that they can be moved and manipulated as one set. Just be aware that after you "remove group" from a group of selected multiple clips on a timeline that has been set up with separate audio and video tracks, all of the clips in your selection will now act as separate audio and video files. Now they are truly unlinked! The only way to get them back is to "set group" on each individual clip.