This is an old thread.
The server was asking for the password because the SSL host was using an encrypted private key.
To my knowledge, the WHM does not give you an encrypted private key. The private keys that the WHM generates will be decrypted:
Code:
-----BEGIN RSA PRIVATE KEY-----
MII...
-----END RSA PRIVATE KEY-----
As long as you install a decrypted private key, it will not ask for the challenge password when apache is restarted.
Just be sure that you use the same private key generated with the CSR that is used to buy the certificate.