The Linux kernel has a SPI driver for Atmel 9260 processor. Maybe you should try to use the SPI driver from the kernel. If you have to write your own and need to use the interrupt you should use the kernel interrupt handling mechanism. You should not change the AIC settings directly in your program. The boot Linux Device Drivers is a good place to find information. Here is the link to the chapter about interrupt handling
http://www.xml.com/ldd/chapter/book/ch09.html