Whatever you want, as long as you don't overwrite the original file.
You should convert your WAV file to FLAC unless there's a specific reason you have them in WAV. Then if you need smaller files for portables or something, re-encode the FLAC into variable bitrate MP3 with LAME, or Ogg Vorbis if your player supports it. Aim for a variable bitrate of around 200kbps average.