The answer is not pretty simple.
Working with sounds in as3 and air is still not an easy task, due to the lack of expressive APIs.
What i suggest you more, that is indeed what i did in the past in a similar situation is to use NativeProcesses as the bridge for a low level language to handle complex task like this.
I'll go with Lame as a good mp3 encoder, and echoNest for handling sounds processing.
What native processes simply does is just start a process outside the air box, and just wait for responses. What you should do is just creating a python script that given two mp3 (previously saved by air on a temp directory) mix it with echonest-remix-api, save as wav and encode as mp3 using lame.