That will get you a WAV file from your .ape file. From there you run anything that will compress the WAV to the format of your choice. I usually run LAME to get an MP3 file, but if you need some ...
rip them to ape format... then if u want to make cds from them later on jsut convert them to wav file (thats loseless to loseless format so theoretically there should be no change). im jsut not sure ...