why not just use CD Wave for splitting both files...
start with the low-res. split the tracks as you normally would in CD Wave (it always splits on sector boundaries, so no worries there). after you save all the tracks, save the .cue file. then open up the hi-res file. then go load up the .cue sheet you just saved. it will then ask you if you want to open up the original file associated with the .cue sheet. hit NO, because you don't want to open up the 16/44.1 version, you want to apply the .cue sheet to the hi-res file. and bam, you're done, just save the new tracks and you're good to know.
this is how I do it, and it's fast and easy. let me know if I should be more specific, or if you're unsure of anything I just said...
- Jason