DS homebrew uses the DS hardware specifically. DSTWO homebrew use the DSTWO specifically. If you're talking about using both at the same time, unfortunately, you can't. The only interaction involves copying rendered images/video+audio form the DSTWO to the DS, and sending input the other way. they would have to design a new interaction API to allow both at the same time.
In light of that, I had wondered if they could specifically have the SNES emulator use both. The game itself running on the DSTWO, while the SPC core for the audio runs on the DS (since it is self-contained and doesn't require anything but input).