I assume you're using windows.. Open command prompt. Navigate to mysql bin folder. Mine is C:/Program Files/MySql/MYSQL Server 5.0/bin. Once in that folder type:
mysql -u USERNAME -p peq
substituting your username, and database name if it's not peq. It should prompt for your password. Enter it, then you should be in, with the peq database selected. You can then type source load_system.sql in or the peq_xxx.sql file.
I'm definitely no mysql guru, but that should work. Again, make sure you backup, unless there's no data worth keeping, then it would be best to just wipe everything and start fresh.
Check out
http://www.eqemulator.net/wiki/wikka...ka=ws992mysql5 or
http://www.eqemulator.net/wiki/wikka.php?wakka=Windows. The sourcing should be much faster that with the GUI. Just switch back after for any other changes if you're more familiar with Navi.