Implementing Cloudflare for server primary domain Without Affecting Other Websites

Hi, I've encountered a challenge with my website (domain.me) where it's experiencing DDoS attacks. To mitigate this, I've decided to set up a Cloudflare account for the domain. However, upon doing so, I've noticed that it's causing all the other websites on the server to become unreachable. I think it's because the domain name (domain.me) serves as the primary domain for setting up the server (domain.me/whm). How to implement Cloudflare for domain.me without impacting the accessibility of the other websites hosted on the same server. Additionally, I'm curious if there's a way to apply Cloudflare settings to the entire server once for all. Regards,