Building sitemap for 2 wordpress install under 1 domain

I have 2 wordpress installs under main domain.

www.example.com --1st wordpress install

www.example.com/blog --2nd wordpress install

What is the best way in wordpress to generate a sitemap for submitting my website to google such that there is no sitemap conflict and SEO penalty for such a setup?

I use yoast plugin and would not mind using other plugin to generate a sitemap. My concern being, will www.example.com sitemap plugin account for the wordpress install in the sub-directory /blog? what if I use the same plugin in both wordpress install. Will there be a huge conflict?

Please suggest the best way to generate a sitemap to help submit my site to search engines.

Thank you very much in advance.

Best,

via Chebli Mohamed