Assuming you're on windows, you'll need to (at least...)
http://wiki.eqemulator.org/p?Complet...top-windows-7-
http://wiki.eqemulator.org/p?Complet...or-windowsnbsp
http://wiki.eqemulator.org/p?Complet...load-cmakenbsp
http://wiki.eqemulator.org/p?Complet...indows-desktop
http://wiki.eqemulator.org/p?Complet...-to-everything
(git and cmake only)
http://wiki.eqemulator.org/p?Complet...ing-the-server
That's a heavy-handed description of what's left..but, I believe those are the only things not included in Akkadius's installer script.
At this point, you will no longer need to download pre-compiled binaries through the script..though, you can overwrite any local compiles by using the script downloads.
Step 4d of "Compiling the server" says to 'compile' the server. You want to make any changes to the source code prior to compiling and copying the binaries.
Additionally, any future changes (including code reversions) will need to be recompiled and copied as well.
EDIT:
If you have never compiled source code, the task can seem quite daunting...
It is relatively easy, however. You can start with just compiling the base source code.
To get your feet wet, you can make little changes to messages sent to the client so that you can see the results of what you are doing.
Visual Studio is fairly decent at telling you what is legal coding syntax.
Code:
char a[8] = "1234567"; // correct
char b[8] = "1234567; // complains about missing closing quote