It is an all-around general type of thing. You use the db and load your eq client. Once in-game, you spend your time testing everything out. Check spawn placement (yes, even npcs facing walls is something that is worth fixing), check if spawns are spawned in the air/on top of one another... see if zonepoints are bringing you where they should.. stuff like that. There is no real method to fixing a db... it's a trial-and-error sort of thing.
I'd suggest using mysql-front (or any other sql editor that gives you sql queries for everything you change) ... then whenever you make a change, copy the sql query down below into a text file, and comment each query with what it changes/does.
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