OK
MySQL Workbench is a design tool (I use it) - I guess you may have backdoored MySQL to work that way.
you have two-three choices
Install IIS (or Apache), PHP and MySQL all standalone (they can be made to work quite well together) - I have two Server 2003 boxes, and they run IIS6 with PHP, Active States Perl, and MySQL running plus one W2K8 server running IIS7, FastCGI, PHP(Zend) MySQL and Active States. So I speak 'Doze' server-ese fluently.
I also have 2 XAMPP boxes, and three Linux servers - one Centos, one Fedora and one RHEL.
so i are the Server Geek, LOLor
Install XAMPP - which gives you all the pieces in one package. (but you will need to unistall MySQL workbench and/or MySQL standalone to make it work right. Basically there can really only be on MySQL instance on a single server without virtualization)
XAMPP is a very good tool, but it is a shortcutted install that will need some fixing. It can do all the things a standard install of Apache, PHP and MySQL will do, with a few tiny possible exceptions (there are a few 'tool' pieces missing that you only get with fill installs) - its built on the Apache Software Foundation's source and binaries. The standalone installs are a more robust solution, and follow best practices -- but require much more integration work/knowlege.
It would be nice to have the XAMPP panel working if only because I like things to work - and getting things to work is how you learn
Haha - that's the engineer talking.
OK uninstall what you did, clean it all up nice, make sure MySQL is not installed or in the service list, the re-install XAMPP (sans the MySQL Workbench)
AND AND - learn a backup product and make daily incremental backups. Acronis Ent. Server is big bucks but it is nearly perfect. (does bare metal reinstalls) At minimum, do a Windows full System backup to another device on the network and make a System Restore diskette (yes diskette) its the ONLY way to restore a Windows Server 2003 to a new drive without 3rd party software
(25+ years systems engineer talking now) One KABOOM and all your work goes in toilet! If you are not doing hardware RAID, or the primary drive is not already mirrored - mirror the drive once things are working.
Good Luck