Will the plugin work for the site if plugin is installed on directory subdomain?

Hello,

If I install Affiliates Manager on the WP installation at a directory-based subdomain (mysite.com/affiliate), will it work for my main WP installation at mysite.com and/or at another directory-based subdomain WP installation, such as mysite.com/woocommerce (for example)?

Why:
As I plan to have many features for the entire website, I must use many plugins. To avoid/minimize the plugins conflicting with each other, I plan to use separate WordPress installations (as in multisite) on directory-based subdomains. The idea is that the same design look for the secondary WP installations, coupled with directory-based subdomain usage URL looks, should allow for seamless integration of each separate installation with each other.

Any recommendations?

Thank you in advance!