You want to change the keys encoding format to either Partitioned-, PGP/MIME- or the new PGP-EML-encoding.
This article refers to keymodes, the way how a key is managed. For further information about keymodes, check the Administrator's Guide or http://www.symantec.com/docs/TECH149029
For server-side-managed keys (SKM and SCKM) this can be changed in the administrative interface of the server. Go to Consumers/Users/ and select the user that has the key you want to change.
Expand the "Managed Keys"-section and check the "Encoding Format" in the middle of the row. To the right you can see some symbols under the column of "Actions". When clicking the pen you can change the Encoding Format as needed.
For client-side-managed keys (CKM and GKM) you can change the encoding format only on the client, PGP Desktop or Symantec Encryption Desktop or automatically via the Symantec Mail Encryptor for iOS, since it prefers PGP-EML.
Check the properties of the key and change the Encoding Format. Enter the passphrase for the key, if prompted.
The client-side managed keys need to be re-uploaded to the server. Rightclick the key and select "Send to" -> "Symantec Encryption Server".
You cannot change the general default encoding format for new keys, which is PGP/MIME.
Symantec Encryption Management Server 3.3.0, Symantec Encryption Desktop