To start with you must export your certificate with the full intermediate chain path into a pfx file. You then run the following commands to copy the certificate and key into the java keystore.
The first command removes the existing certificate, the second one (with command output) will show the certificate alias within the pfx file. The third one will copy the key into the ahsay keystore. You will need to restart ahsay to get it to start using the new certificate and key.