Lyx support including/inputting a file from another directory, but this fail if the included file includes more files (such as figures) from its own directory. This because latex don't acutally change into the subdirectory.
This is a problem when writing large documents (i.e. books), because having a subdirectory per chapter is so convenient. The problem is solved for latex by using the import.sty package. The problem is also solved for lyx, by using my patch that makes \subimport* available through the lyx GUI in addition to the existing \input. More information at http://www.aitel.hist.no/~helgehaf/sw/sw.html Download for 1.2.2 patch http://www.aitel.hist.no/~helgehaf/sw/lyximport122.diff Download for 1.2.0 patch http://www.aitel.hist.no/~helgehaf/sw/lyximport.diff Helge Hafting