Are you asking about user certificates to use for authentication? If so, note the release notes tell us:
Certificates imported using Legacy AnyConnect version 4.0.05x and any earlier release, cannot be accessed or used by the new AnyConnect app release 4.0.07x. MDM deployed certificates can be accessed and used by both app versions.
Reference: http://www.cisco.com/c/en/us/td/docs/security/vpn_client/anyconnect/anyconnect40/release/notes/b_Release_Notes_Apple_iOS_AnyConnect_4-0-x.html#topic_178115CFD22D4817A62462A331BFEBC8
If you need to import a user certificate then you can do so in the app under Diagnostics > Certificates > Import User Certificate...
Server certificates will of course use what the server presents.