Basically, I write everything using relative pathing so it is portable, and it works great with a single level of aliases, but add the subdirectories in there and all of a sudden no style sheets, images, or anything can be located properly, and I get unstyled, pure XHTML output.
That sounds like it is working just like it should-- you cannot use subdirectories in your path and relative URLs at the same time.
The reason is that if you go to /subdirectoryalias/index.html and then use relative paths in your template to "css/style.css", the browser on the client side correctly assumes that the actual path is /subdirectoryalias/css/style.css", which, of course, doesn't exist.
I don't see a way around that because according to the RFCs, this is exactly the behaviour that the browser should be doing.
I tried changing everything to absolute paths (relative to the server root) and had no better luck.
This I don't get because it works for me: /assets/sites/style.css always works, even with aliased paths like /work/projects/thissite/changes.html
Or am I misunderstanding something?