Just to be explicit, there is no need to have SqueezeCenter* see both the FLAC and MP3 files, because SqueezeCenter can transcode from FLAC to MP3 on the fly. So clients that can't play back FLAC can get MP3 streamed to them instead.
The need to keep MP3 versions along side FLAC is generally to support portable players which have limited storage capacity and also may not support FLAC. Special care needs to be taken in this circumstance because Slim Center doesn't come with any built-in ability to make managing this type of duplication painless.
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