Check this thread:
http://www.subsim.com/radioroom/showthread.php?t=97851
which details a method for adding persistent comments that will show up in the in-game Captain's log (KTB).
Unfortunately, SH3 Commander doesn't pick up these new entries and put them in the Personnel File it creates for your Kaleun. Maybe someone more familiar with how SH3 Commander works (maybe even JScones) could explain exactly where/how SH3 Commander looks to your game's log files to generate its personnel file and figure out a way to pull in these new log entries into the personnel file - would be a great addition
There was mention a few weeks ago of some possible work by JScones to add at least some rudimentary log capability to SH3 Commander in another thread, but nothing seems to have come of it to date and the thread seems to have gone cold - see here:
http://www.subsim.com/radioroom/showthread.php?t=97547