Well the first and major pitfall is with filenames.  It is important that you keep organised when ripping.  This is particularly true if you have a lot of classical music.  The worst case scenario is ripping a CD with Baroque Concertos where the file names are "Allegro", "Adagio", "Allegro" etc.  Your PC will overwrite filenames with the same name so in worst case scenario you might finish with only two tracks.  To avoid this

• Create a folder structure to hold the music, then add subfolders for artist/composer and sub sub folders for album"
• In EAC Select EAC/Options/Filename and enter %T - %N whic will rename each track with the original name plus a unique number

  That way you won't have duplicate file names.

Next in EAC/Tools  select "Start external compressiors queued in background" and set the number to 3-4

In EAC/Extraction set Error recovery to High

In EAC/Compression Options/External Compression you will need to add the line -8-T "artist=%a" -T "Title=%t" -T "album=%g" -T "date=%y" -T "tracknumber=%n" -T "genre=%m" %s then set the Use File Extension to.flac, the Parameter passing scheme to "UserDefined Encoder, then include the path to where FLAC is stored on your PC.  Set the bit rate as high as possible, check Delete WAV after compression.

That should cover EAC so we need to make a quick adjustment to FLAC  The compression rate should be set to 8.  This slows things down a little but it does save space.

Does that help?  I'm sure others may have tricks to share.