it can be very frustrating, believe me i know! but dont give up! keep at it and it all becomes more and more clear over time.
a suggestion if you havent tried it, try the
peq serverpack installer.
http://www.projecteq.net/phpBB2/viewtopic.php?t=4346
and the self-installing updates are here(just need the most recent i believe?)
http://www.projecteq.net/phpBB2/viewtopic.php?t=4612
they will make the server setup unbelievably easier.
for your edits aside from the mysql tool you are already using (which is ideal for many things but clunky for others) try using GeorgeS tools are they are nothing short of badass in every regard.
http://www.eqemulator.net/forums/forumdisplay.php?f=674