I recently instituted Cloudflare content delivery network, which in involved pointing my nameservers at them.
I know now I have to use "direct" in my path to my FTP, i.e. http://direct.cirrusimage.com.

What root path do I use for sitemap generator?

The same  address you use as when browsing your website using an internet browser, i.e. most likely the same as always

As far as I know, Cloudflare is entirely a "back-end" solution, but does not change anything for outside crawlers, human visitors etc.

Do take care though that Cloudflare may throttle/ban traffic from IPs "overloading" the website. You may need to somehow configure Cloudflare to allow your IP/A1SG to crawl the entire website. (I would only bother with this if it becomes a problem, most likely it will not be necessary.)