I have added support for the import package to my lyx 1.2.0 source. I have created a fourth option in the Include inset for this, that lets me import a lyx file from a subdirectory. This lets me use a directory structure with one directory per chapter for a book.
Doing that with "input/include" cause trouble whenever the included file tries to use graphichs. I wonder if there is any interest in this - should I create a patch and post it here, or put it on a web page? My current approach creates a \lyximport{dir/file.tex} command. A simple latex package translates this to \import{dir/}{file.tex} which the import package uses to successfully import from subdirectories. Having lyx create \import{dir/}{file.tex} directly is of course a better approach, avoiding the translation latex package. Generating such output seems easy enough, but I am not sure about reading back a two-argument command for presentation in the inset. Helge Hafting