We do include SQL changes with the downloads now :P I am guessing that you didn't see that we now use google SVN for handling update releases. The 1129 version is very old now. We are 450+ revisions past that point now on the SVN. You can get the newest versions here:
http://code.google.com/p/projecteqemu/source/list
Also, PEQ keeps up to date with that as well. Once the PEQ site is back up, you can get the correct database version to match the latest available Binaries download. They both work together without requiring any additional changes. And, after that point, you can always check to see if new SQL files were added to the /utils/sql/svn/ folder and source them when you update your source code/binaries.