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You shouldn't convert an mpeg1 file to mpeg2. This WILL give you poor quality video.
What are your capture settings?
You should capture with mpeg2 and use a minimum of 44,100KHz for audio.
It sounds like you have a low quality mpeg that you are trying to make better quality. This is not possible.
Remember: your can never make it better then the original source. You would be better off to capture at a really high res/quality and then use TMPGEnc to bring back to the spec you want it.
If you still have the Original Mpeg file then use the audio from that..Just demux the original Mpeg files audio then mux it with the New mpeg file, the Quality should be better..But I agree with Gamer the Quality of a Mpeg file encode to Mpeg again will be Quite bad...
If I understand your post correctly, your mp3 file is unrelated to the file that you've converted to mpeg2. In other words, you're completely replacing the audio.
If that's the case, convert the mp3 to a wav file then enter it as the audio source along with your original mpg file for the video.