Which one does the SSL key file go in?
The ssl key is generated and managed by ispconfig, so there is no field for it. Just createa new ssl cert trough ispconfig and then use the csr that ispconfig created for you and let it sign from the ssl authority.
So the steps to enable ssl for a website are:
1) Check the ssl checkbox in the site settings.
2) Create a new self signed ssl cert in ispconfig on the ssl tab.
3) Let the csr sign from a ssl authority and paste the cert into the sl cert field and choose save.
All ssl authorities lat you resign a cert, so you could reissue your cert based on the ispconfig csr.
Thats also described in detail in the ispconfig 3 manual.