The Meaning of Life, the Universe, and Everything.
All minecraft worlds contain 3 files: one for the overworld, one for the nether, and one for the end. In your files saves for a world you should see a "region" folder a "DIM1" folder and a "DIM-1" folder. Region contains the region files for the overworld, DIM1 contains the regions for the End, and DIM-1 is where the files for the Nether are kept.
The new folder structure you're seeing is how it re-formats itself for SMP. If you want to port your old save into a new SMP world I would start by creating an SMP world making sure that it is being generated in the same version and with the same seed as the world you wish to import. Once you start the server and it creates the file structure, I would shut it back down place the appropriate region files for each SSP dimension into its appropriate SMP file folder. When you restart and join the server it should load your existing region files into the world and use the seed to generate new terrain when leaving those ares so it doesn't look terrible from a seed mismatch. Hope that helps.