From the topic title, I am afraid you would still have to make sure your naked (main) domain like yourdomain.com nameservers are pointed to Cloudflare nameservers. To make use of Cloudflare services, you need to change the nameservers for your entire domain.
Therefore, at Cloudflare Dashboard on the DNS tab you could just switch off the proxy status to (DNS-only) for yourdomain.com and www.yourdomain.com DNS records, while keeping the proxy enabled only for your sub-domain for example like sub.yourdomain.com or any other.
From this point, for any further need you would manage your DNS records at one place, Cloudflare.
In a better case, I would suggest having your naked domain proxied too, why not?
Furthermore, if you want to add only the sub-domain to Cloudflare, unfortunately that won’t work and you would have to add the root domain as you would encounter an warning/error like add the root domain at the first step of getting started with Cloudflare.
There is a possible way, you could sign up for a Business (or Enterprise) Plan and then use Cloudflare in a CNAME setup, as described in below article: