So theirs /sitemap.php , sitemapindex.xml But which one is the best to submit to Google in Google webmaster tools?

Also, what is the proper way to clear the cache, and re-build the sitemap?

thanks

If you're using url rewriting, then submit sitemapindex.xml. The idea is to submit the same link you display in the forum footer for consistency. But both will work.

About cache refresh, it's up to you to decide how often they should be refreshed, automatically or not, in acp. By default, sitemaps are automatically refreshed every 24 hours, but you can use a shorter period of time (below 6 hours has no meaning in much cases IMHO) if your forum is very busy.

++

thanks!!!