After you identify the problem space, you can attack the potential origin of the problem. Often, this will involve reviewing log files on your server. Linux has great logging, and many of the applications you may be running are writing log files as events happen. If there's an issue, you may be able to find information about it in an application's log file.
Inside the /var/log directory, you'll see a handful of logs you can view, which differs from server to server depending on which applications are installed. In quite a few cases, an installed application will create its own log file somewhere within /var/log, either in a log file or a log file within a sub-directory of /var/log. For example, once you install Apache, it will create log files in the /var/log/apache2 directory, which may give you a hint as to what may be going on if the problem...