You'll never get SBE's with CD Wave. Use it as the last step.
Well, I used to do this, but it really created a lot of extra work when doing both 24 bit and 16 bit. Now, when I encode the 16 bit WAV files to FLAC (after I've resampled and dithered the individual tracks), I just select fix SBE's in TLH.
I did use it as the last step except for encoding to FLAC. I used TLH to check for SBEs and it said only the last track had and SBE (which is normal at the end, right?). So what else could it be if not and SBE? Something related to resample or dither?
You are only worried about the last track showing an SBE? I'd say don't worry, but if you don't want any to show up, just use a small track split at the end and unselect that last track when you save the individual WAV files in CD Wave.