Edge, i'm sure it worked for you because in inadvertently did it correctly. i'm quite sure it wouldn't have worked otherwise.
when it comes to patching software manually (cuz we're all so used to the auto-downloaders / patchers in today's world) it pays to be familiar with the way a program organizes itself. Sometime just for fun take a look at the different folders under the main Everquest folder. Explore into them to see what's inside of them. Don't necessarily mess with anything, but it'll give you a little knowledge of how to fix things when they break, or how to install custom stuff. In this case you'll notice that the hotfix extracts 2 folders. Looking at the contents of the main Everquest folder you will see that those same 2 folders already exist (along with others, of course). You'll also notice that the files inside the 2 hotfix folders also already exist inside the folders inside the main Everquest folder. (lost yet?) Thus, when you cut/copy and paste you are replacing the old with the new....also known as updating.
and i'm spent.