See http://www.aitel.hist.no/~helgehaf/sw/sw.html for a patch that lets lyx (1.3.0 and 1.2.x) include files from subdirectories.
This is useful mainly when writing something large, like a book. The patch makes it possible to have different chapters (or parts) in different subdirectories. This is possible with plain lyx only if the files in subdirs don't include any more files (or graphichs) on their own. The problem lies in latex, which need the import.sty package for this to work. My patch add an option to use import.sty as an alternative to include/import. Helge Hafting
