I run Google XML Sitemap on a WordPress 3.0 with network enabled and 3 different website.
i activate the plugin (version 3.2.3) as “Network Activate” and configure the plugin in all the site as following
for the main site https://www.myndd.com/ :
–Location of the sitemap :
—Automatic Detection
for the 2nd website https://www.myndd.com/en/ :
— Location of the sitemap :
—- Custom Location
—— Absolute or relative path to the sitemap file, including name.
——— /home/myndd/public_html/sitemap-en.xml
—— Complete URL to the sitemap file, including name.
——— https://www.myndd.com/sitemap-en.xml
for the 3rd website https://www.myndd.com/wathever/ :
— Location of the sitemap :
—- Custom Location
—— Absolute or relative path to the sitemap file, including name.
——— /home/myndd/public_html/sitemap-wathever.xml
—— Complete URL to the sitemap file, including name.
——— https://www.myndd.com/sitemap-wathever.xml
and you can do this for all site on sub-directory or sub-domain…
then you just add all the sitemap (https://www.myndd.com/sitemap.xml, https://www.myndd.com/sitemap-en.xml, https://www.myndd.com/sitemap-wathever.xml) to your Google / Yahoo / Etc Webmaster Tools
si is not perfect but it can help you before Google XML Sitemap 4.0