i like to do all my tracking at the very end of everything. i record at 24/48, and my process is like this:
1. apply any necessary audio adjustments (for example one of my channels got turned down by a beeyotch standing on my case at mule the other night, so my first step is to apply gain over the section on that channel so it matches the rest of the recording)
2. resample to 44.1 (using sound forge at highest accuracy setting with anti-alias filter)
3. bit-depth conversion (again in sf, currently using highpass triangular dither and high-pass contour noise shaping, though i don't know the difference between that and other settings)
4. save new 16/44.1 file with new name (i keep all the 24bit recordings for archival)
5. open 16/44.1 file in cdwave, track, save cue file, open it on the 24/48 file and track that too
6. flac
tadow.