Im not sure if Im asking the right place, but basically Im looking for advice on the best way to:
Record Audio through a microphone on a website and Upload the audio
Use Adobe Flash Media Server (http://www.adobe.com/products/flashmediaserver/) or Java servers with support of incoming sound streams.
With FMS it is realy simple. You create in flash swf-app that reads microphone and send sound stream to server. FMS will write it as .flv automatically. You should find few samples answering yours problem in Adobe documentation.