2 Super Cache on 1 server / 2 wordpress sites

Wordpress 4.7.5
we have 2 separate wordpress sites on 1 hostgator reseller server.

domain.com (which doesn’t use its blog)
domain.com/blog (which is the blog)

there are separate installations, with separate MySQL databases.
(NOT a multi-site install)

I’ve tested WP Super Cache on domain.com. (had to remove it for a major theme update, but looking to install again).

Question is:

To cache both sites, I assume we need to install WP Super Cache on both wordpress sites with different Cache locations.
But will this cause conflict or performance issues? Especially given the domain and domain/blog?

Also your FAQ mentions a WP Super Cache plugin update deleting settings because they’re stored in the plugin folder? Or did I read that wrong? FAQ had text around creating a different folder for settings somehow, but it was unclear.
Since I’m talking about 2 Cache installs, I’m trying to understand this FAQ comment and how it pertains to a double cache setup.

FYI… both WP sites also run Yoast and WordFence. (I’ve read about the Yoast/WP Super Cache XML Sitemaps workaround). and Avada and Minimaze themes.

Thanks