Im way lost in the shntool realm but Ill save that for another post.
if you use cdWave for tracking all splits should be fine with no sector boundry issues, so I would suggest using mkwAct to convert to .shn, it is really really easy
if youre new to this, id say flac it, same/a lil better compression, pplus, a huge thing for me, is the md5's are GONE,and its all in one EASY,EASY step
youd just go from your finsished/tracked cuts and open them in flac, and hit 'encode' really easy w/ one button to hit, plus, im a phlack phluffer, and its the shit