I own a site that has 3 sub-directories, all separate WP installations. I am using the Google Sitemaps plugin on all of them (including the main one) and hence have 4 sitemaps in total. So it's like abc.com/sitemap.xml, abc.com/subsite1/sitemap.xml, abc.com/subsite2/sitemap.xml and so on. I have mentioned all of them in my robots.txt file.
A friend of mine suggested that this may not be the right way to go about it because Google will still consider it as one site,since the TLD is same. Hence, it's better to figure out a way to have a single sitemap for the all the sites.
What do you say? Is he right?