You delete entity beans via their home or component interfaces. The method you use is called [unsurprisingly] remove. Its signature is remove() in the home, and is overloaded in the component so it is remove(Handle handle) and also remove(Object key).
Updates are done by setting the CMP / CMR fields to their new values, the container is tasked with keeping this information synchronized.
The container will then reflect these changes in the database, and should delete or modify the row(s).
For examples, have a look at Ed Roman's Book, Mastering Enterprise JavaBeans.
Mastering Enterprise JavaBeans