If you check the option "Overwrite any existing DNS zones for the account", cPanel will overwrite the DNS zone for your main domain if it exists on the server.

What happens if I don't check it (so the account is created to use my nameservers), but they don't change anything at their registrar? It doesn't seem like it would do anything in that case.
It won't do anything in this case because the domain nameservers will still be poiinting to the old location and you can modify your DNS records in the DNS zone on the servers where your nameservers point.