I have one site, let's say www.site.com, i submitted the sitemap to google and everything it's ok, in www.site.com i made www.site.com/secondsite/, a different script but releated with the main site, the question is ..I can submit my folders sitemaps to google for a better index ?
I think this may need more clarification as to what exactly you are looking to do but if you mean placing www.site.com/secondsite/ in the sitemap instead of www.site.com/secondsite/index.htm then yes, you can.
A site map is used to submit the URLs needed to index the site completely. But unless you give Google a page with all dynamic urls on it with the associated query strings needed, these pages will never be indexed. But when you go to a "subsite" like what your are describing, then yes you must create a site map with urls and associated query string. Google will allow you to submit multiple sitemaps for a single domain (i.e. French, Germal, English, ets.)