Here is what you need to customize the layout of a virtual keyboard:
1) Get the decode_vkb perl script. You use this script on the appropriate VKB file in /usr/share/keyboards to convert the VKB into an editable XML document.
2) Get both deb from here for the appropriate architecture (depending if you are doing this on the device or on a linux x86 workstation). Use ar and tar to extract the files from the deb, and then to extract the gen_vkb executable and the libimlayouts shared object from the installation archives. Put them both in the same folder -- to run you need to add the current path to LD_LIBRARY_PATH.

Now you have the tools. Simply decode the VKB to XML, edit the file, and then re-encode it using gen_vkb. Move the generated .vkb file to /usr/share/keyboards, restart the hildon-input daemon and voila!

I have modified the en_GB virtual keyboard so that it uses the Fitaly layout. This worked well under OS2007, but with OS2008 the "baseline" attribute in the keysizes block does not appear to work -- so the keyboard isn't as nice.

Documentation is somewhat sporadic, but here is what I found:
1) maemo-dev list

Hope this helps,

Robert B.