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Everywhere I read says to have the server hostname in the commonName field and the subjectAltName field. The problem is that the hostname that I want to sign has greater than 64 characters. Therefore, the hostname wont fix in that field. I have seen sites such as this which even say that it is a security vulnerability not to have the hostname as the commonName. How should I do this?

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Check this RFC:

This previous questions at stackoverflow:

As for a workaround, you can set a short CNAME entry in your DNS.

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That wont work: the reason being that the hostname is a sha2 hash, I cant shorten it without losing meaning. – chacham15 Apr 14 '13 at 8:42
up vote 0 down vote accepted

THe answer is that the cname is only an alternate. The cname and the san dont have to match.

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