If want to have a sitemap, you actually need two of them in your case, as both will include different links from different parts of your website (Magento-based and Wordpress-based).
You don't need both sitemaps in the root. Your wordpress sitemap can be in the "resources" directory , as the only restriction is that sitemaps cannot refer URLs higher in the directory tree. As all your wordpress URLs have "resources" as their base, there is no problem here.
To notify Google of your sitemaps, add your site to Google Webmaster Tools (http://google.com/webmasters) and go to Site configuration / Sitemaps. From there, you will be able to both test your sitemap, add it, and later, when already added, you will see its indexing rate.
You will also gain a lot of valuable insight by adding your site to Google Webmaster Tools, so you should do it anyway.
If you have more questions, I will be glad to help you further.