How can I change the paths were Boost.QuickBook looks for the following files?
1) CSS and icon images by default from BOOST_ROOT/doc.
These are Docbook XSL params rather than anything Boost sets: html.stylesheet - sets the name of the stylesheet (including any relative path). Not sure what you mean by icons, but the admonishment graphics path is set with admon.graphics.path See http://docbook.sourceforge.net/release/xsl/current/doc/html/index.html for a full list of options. Assuming you're using a Jamfile to build the docs, then these are set with a <xsl:param>parameter-name=value In the build options for the documentation target.
2) Navigation bar by default from BOOST_ROOT/tools/boostbook/xls.
That I don't know how to do - you can certainly disable it (don't ask me what the xsl param name is though - you'll need to look at our stylesheet customization layer for that). In all likelihood you'll need your own XSL customization layer - I'm not sure how you integrate that with Boost.Build though. HTH, John.