Difference between <system.web> and <system.webServer>?
The system.web section is for configuring IIS 6.0, while the system.webserver version is used to configure IIS 7.0. IIS 7.0 includes a new ASP.NET pipeline and some configuration differences, hence the extra config sections.
However...
If you're running IIS 7.0 in integrated mode only, you shouldn't need to add the handlers to both sections. Adding it to system.web as well is a fallback for IIS 7.0 operating in classic mode, unless I'm mistaken. I've not done extensive testing on this.
See http://msdn.microsoft.com/en-us/library/bb763179.aspx for more information.
The former is for Classic Mode.
The latter is for Integrated Pipeline Mode (available in IIS7+).