It is hard to advise completely because I don't know your setup, but either way, regardless of the approach you take, you will have to do the same thing.

You will need the frontend to proxy the node server back end.

So, if nginx is your frontend, you would set a reverse proxy to the port you are using. No need to create an actual sub domain. The configuration can be done in nginx config files.

In cloudflare, you add a DNS record, jot.domain.tld and point it to the IP of either your current server, or the new one.

If you are using a control panel that auto creates the let's encrypt SSL and you need the subdomain to do so, creation is fine. You still must reverse proxy node.js