macromedia flash flashcom: How can we combine(overlap not concatenate) flv audio streams on server side in one flv file?

FMS can't do that. You'd need to use a third party program to mix the streams
to a single file, but I don't know of any that do that programatically.

No support for synchronizing streams has been a shortcoming of FCS/FMS since
day one. Hopefully future versions will address that.