You must enable custom (authoritative) DNS servers in the CCP and add your IPv4 and IPv6 addresses of `ns1.mydomain.com` and `ns2.mydomain.com`.
In order to do so, the two nameservers must also serve DNS records for `mydomain.com`. Otherwise, netcup's system will refuse to propagate the entries to the authoritative nameservers of the `com` TLD.
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Does it mean that if I enter host ns1.mydomain.com IP address 3.3.3.3 in the control panel, the Netcup panel's software will first query 3.3.3.3 to check if it serves mydomain.com before allowing the entry to succeed?
Exactly.
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If so how can check that the nameserver IP address I've been assigned by the service provider will reply whether or not it has been configured to serve my domain, eg query 3.3.3.3 to see if it provides name service for mydomain.com.
For example, run `dig mydomain.com NS @3.3.3.3` or use an online DNS resolver website (if such a thing exists?).