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Yes, ffmpeg can separate the audio and merge it back. But I don't want the video I was using it as an example on how bad an audio I have sounds like. I did try the equalizer from audacity to improve the audio but it had little effect. I guess it is hard to fix some things when you don't have the original source.
There are (at least) two different things wrong with the audio in that YouTube video. First is the muffled sound, which is to say that the high frequencies are weak. This, by itself, would be correctable by bass, midrange or treble adjustments, or an equalizer. The second problem is the hiss (white noise). If you simply turn up the treble to correct the high frequency range, the hiss will sound even worse.
So you will probably need to try "Noise Removal" first. See if you can reduce the hiss without distorting the voice/music signal too much. Then correct the bass/midrange/treble.
You said the YouTube video is just an example. If your audio clip doesn't have that much hiss, that is, if it is muffled without the hiss, it will be easier to improve the sound quality.
That person has all six seasons of Mr Belvedere in his youtube channel and only a few have bad audio. It's good to find old shows because they were great.
If you want Mr Belvedere, buy the DVDs. If for some reason you dont/wont/cant pay for the DVDs, try finding the shows somewhere else. D/ling from youtube is just as 'illegal' as d/ling from some filehost, and you might as well get a decent copy. Why try to fix some dodgy TV rip when there will be DVD rips around........
I don't think you can use Audacity to work in streaming mode. You'd have to download either the audio for both video and audio and then try to work on it.
There are some very advanced tools to work with audio and video but only a few are opensourced. Audacity can only use filters that have been made but generally the tools need to be used on good quality source. You could in fact modify very short sections at at time to fix or try to fix the quality. The process would take weeks or more.
Distribution: Debian Sid AMD64, Raspbian Wheezy, various VMs
Assuming you mean that your sound file is quiet like the clip you might want to try gain also this basically amplifies the sound in the file. Of course it also amplifies the noise so Beryllos's recommendation of noise removal is a good one.