"go back to my original files, encode for the correct bit rate, etc., create MP3s that all match the web site's specification, then if I decide to add any audio FX, I'll do that will the supposedly correctly created MP3s."

Actually you are best to work not with the mp3 files but the full wav style files - every time the conversion is done, there is a potential loss of quality. When you are finished all audio processing, then encode MP3s that all match the web site's specification.