Here’s an application note from Atmel: Using the WeX timer/counter extension (PDF!)
This application note describes the various functions of the Waveform Extension (WeX) to Timer/Counter 4/5 available on the Atmel® XMEGA® E. It details the differences and improvements according to the AWeX extension to Timer/Counters of the previous XMEGA (see AVR®1311 Application Note). Included are code examples to simplify the use of WEX in typical applications. All the software examples mentioned in this cookbook are provided in ASF (Atmel® Software Framework).