Basically you pickup sources from SVN via Eclipse, and use Eclipse to do you own modifications and/or compile.
What you surely got is a preconfigured pack, aka a pack which is already compiled. You can't change a shit about it, except DP.
So in that order :
- Dl eclipse and install it
- Install subclipse and parameter SVN to L2J SVN.
- checkout (download) what you want.
- compile directly and install.
Once you did all that and got a working server, you only have to open eclipse, do your modifications i core, compile, and update l2jserver.jar when you need.
There are tutorials on the wiki so far, read http://trac.l2jserver.com/wiki