So, here's some pics of what I did here. I basically stole the idea from the double-wide Wario Ware Twisted case. Sanding down the edges of the two cases on the sides where they join, cutting a hole out of the center and bolting the two together. One minor change is that I had to cut part of the DS game card slot out of the back case - the knob of the paddle controller hit it. Then, I had to cut out a little more because I didn't like the way the case rubbed against the edges of the knob. You can see in the last photo, the knob does - barely - cause the plastic to bulge out a bit...
Here's the front part of the case:

Here's the front part of the case with the paddle controller in it:

And the back-half of the case:

And the back cover, taken from an angle to show the bulging knob controller:

The pic makes it look worse than it is...