I'd recommend using phpMyAdmin for starters.
MySQL also has a program called MySQL Workbench that you can download from the main MySQL site here: [dev.mysql.com
Unfortunately it requires .NET 4 which you can download here: [microsoft.com
recommend enable logging of MySQL queries (you should also be intimately familiar with Apache's access and error logs).
MySQL has a "my.ini" file for configuration however you can use MySQL Workbench to enable logging albeit to the database while I prefer a file myself as if the MySQL service becomes unavailable I can still access a regular file. You should be able to change these around if you want to set them manually...
log_error = "C:/mysql/data/mysql.err"
pid_file = "mysql.pid"
general_log = 0
general_log_file = "C:/mysql/data/mysql.log"
slow_query_log = 0
slow_query_log_file = "C:/mysql/data/mysql-slow.log"
...or in MySQL Workbench...
1.) SQL Development.
2.) Open connection (localhost), save the password.
3.) Server Administration.
4.) Adopt the already tested connection.
5.) Once admin tab is open go to Options file under the CONFIGURATION header on the left menu bar.
6.) Go to the Log tab.
Now logs are great and all but what you really
want is a log viewer that will empower you to quickly track things down such as MySQL write commands or HTTP error codes in the Apache access log for example. I highly
recommend Tail for Win32. Go to Settings [menu], Keywords and add terms such as 403, 404, 500, DELETE, INSERT and UPDATE along with colors. It's a real time log viewer (there is sometimes a delay of upwards of 20 seconds on rare occasion I've noticed). It's not entirely perfect, it just opened minimized and I had to right-click and maximize it to make the window viewable. Still it's a very powerful tool despite a couple flaws.
Do all that and you'll be ahead of what most people are working with. :)