При чем тут array?

ДокаA stream of audio data, as might be read from or written to a file, is represented by an AudioInputStream object. (AudioInputStream inherits from java.io.InputStream.)


И наложить на него

Тогда это нужен mixer (возможно програмный) который умеет такое делать.

ДокаIn the Java Sound API, devices are represented by Mixer objects. The purpose of a mixer is to handle one or more streams of audio input and one or more streams of audio output. In the typical case, it actually mixes together multiple incoming streams into one outgoing stream. A Mixer object can represent the sound-mixing capabilities of a physical device such as a sound card, which might need to mix the sound coming in to the computer from various inputs, or the sound coming from application programs and going to outputs.

IMHO

И в чем проблема? Кодируй.