XMega bootloader - How to make use of the functions in assembly source file
The functions in the assembly file are just like any C functions that get linked by AVR-GCC when you include the sp_driver.S and sp_driver.h files and call those functions from your bootloader code. For instance, put this in your main code's header file:

#include "sp_driver.h"

and then call any of the functions from sp_driver, e.g.

SP_EraseApplicationPage(Address);
 SP_WaitForSPM();

Make sure the sp_driver.S is included in the compile list so the compiler and linker can find it.