Merge a flv with mp3 without replacing flv audio stream using FFMPEG

Question 1

Assuming both inputs contain stereo audio you can use the amerge audio filter to merge both stereo streams into a single four channel stream, then use the pan audio filter to combine the appropriate channels into a single stereo stream:

ffmpeg -i video.flv -i audio.mp3 -filter_complex \
"[0:a][1:a]amerge,pan=stereo:c0<c0+c2:c1<c1+c3[a]" \
-map 0:v -map "[a]" -c:v copy -c:a aac -strict experimental -shortest out.mp4

The video can be stream copied (depending on the input video format) as shown in the example if you do not need to re-encode it, but if you must re-encode then see the FFmpeg and x264 Encoding Guide.
The example uses the native FFmpeg AAC encoder which requires -strict experimental (or the alias -strict -2). See the FFmpeg and AAC Encoding Guide for information on other encoders.
The option -shortest will finish encoding when the shortest input stream ends.
See Manipulating audio channels with ffmpeg for more examples.
Make sure you're using a recent version of ffmpeg. See the FFmpeg Download page for builds for Windows, OS X, and Linux.

Question 2

As of the ffmpeg documentation you may use the amerge filter

http://www.ffmpeg.org/ffmpeg-filters.html#amerge

ffmpeg -i input.mkv -filter_complex "[0:1][0:2][0:3][0:4][0:5][0:6] amerge=inputs=6" -c:a pcm_s16le output.mkv

Question 3

FLV does not support multiple audio streams. Technically is is possible in the binary format by incrementing the stream id. However the FLV documentation says the stream id should always be 0. so even if you did create this file, most players would not play it.