I'm really confused,When I choose cryptography service provider for certification authority (RSA # microsoft software key storage provider), why again should I choose rsa algorithm at new certification template? What is the difference between them؟
When you install CA service, you specify cryptographic settings for CA certificate itself (cryptographic service provider, key algorithm, key length and signature algorithm).
When you configure certificate template, you specify provider name and public key algorithm for certificates issued by this particular certificate template. They don't need to match CA certificate cryptography settings. Regarding signature algorithm in certificate templates: this setting specifies the signature algorithm used to sign certificate request. Nothing else. It may not match issued certificate's signature algorithm, because certificate signature is controlled by CA server.