One example of a high(er)-level API in BouncyCastle would be the CMS (Cryptographic Message Syntax) package. This ships in a separate jar (bcmail) from the provider itself, and is written to the JCE (The C# version is written against the lightweight API however).
"Send a confidential message" is implemented, roughly speaking, by the CMSEnvelopedDataGenerator class, and all you really need to do is give it the message, choose an encryption algorithm (all details handled internally), and then specify one or more ways that a recipient will be able to read the message: this can be based on a public key/certificate, a shared secret, a password, or even a key agreement protocol. You can have more than one recipient on a message, and you can mix and match types of recipient.
You can use CMSSignedDataGenerator to similarly send a verifiable message. If you want to sign and encrypt, the CMS structures are nestable/composable (but order could be important). There's also CMSCompressedDataGenerator and recently added CMSAuthenticatedData.
