Cross-posted from my reply to your question on isboxer.com:
Quote Originally Posted by lax
if i wish to be able to run with main in full DX11 am I stuck with 6 installs or to run inner space at all i have to have all on DX 9 ?...
No.. that guide says DX9 because it's from before the DX11 support was added to Inner Space. The only difference for DX11 is that, currently, you need to be on the development build of Inner Space because the DX11 support has not been pushed to the live build. There is absolutely no difference between them as far as using multiple or single folders, and if you can run one in DX11 mode you might as well run them all in DX11 mode.

If you want to run DX11, follow the instructions here to switch to the dev build: http://isboxer.com/forum/viewtopic.php?f=22&t=774
Then just switch the game to DirectX11 instead of DirectX9.

DirectX10 is NOT currently supported.