The low level methods have just a thin layer of code between them and the AWS API itself. Usually they do the authentication plumbing, XML response parsing, and such. You may pass a lot of raw information directly to these methods. They are mandatory in order to actually use a remote call.
Some helpers, such as some of the helpers of the S3 Client, wrap the low level calls for more usability. In fact, most helpers just wrap functionality that otherwise would be cumbersome to achieve just with the low level methods themselves and the client interface.
They are the opposite of the helpers, which generally are optional methods. The only notable exception is client.setCredentials() in certain cases where the credentials aren't provided when the client is initiated.