If you want the highest quality files for the space, use a different ripper, one that will use the CLI version (backend) of LAME with its --alt-preset switches. I personally use
Exact Audio Copy for getting bitperfect rips and used to use LAME with --alt-preset standard (I now use Psytel's AAC which is the AAC equivalent to LAME for MP3s). For a wealth of information, run searches at
the Hydrogen Audio forums.
If you wish to stick with CDex, try enabling the CD paranoia option in it and see if it makes a difference. Also, for the best efficiency, always use VBR. It runs the music through a psycoacoustic model based on audiophiles' ears to get the best quality out of a bitrate. Also do not use 48KHz sampling rates for music as music from redbook audio CDs is sampled at 44KHz. It would be a waste of space and could reduce sound quality by upsampling to 48KHz. However, 48KHz audio is what DVD movies are sampled at so it should be used only with movie files which will be later joined with their respective video files (not movie soundtracks on CDs though, they are sampled at 44KHz just as any other CD).