Crosscompiling / Default configuration

Hello,

since my application is build on another system then it is executed, the path 
of installation makes problems for me.
When compiling matchbox I use
	./configure --prefix=/home/rh/eli/rootfs/usr .....
which installs matchbox at this location.
But when I'm installing matchbox on my embedded box, the installation path 
is /usr, of course. The result is, that when I'm starting 
matchbox-window-manager I get error messages, because matchbox is looking for 
configuration files in /home/rh/eli/rootfs/usr/share, which actually does not 
exist.

Are there config options to overcome this or can I change this in 
configuration files on the target host?

Thanks, Roland

BTW:
Where can I find default configuration files (f.e. for .Xdefaults or session)?