Quartus SOPC Builder doesnt Recgnize my .elf file

Hi, I am using Excalibuer FPGA with ARM 922T I need to download my Digital Design and My Embedded Code on to the chip for which the SOPC builder is not recgonizing my .elf generated by ECOS(RTOS). I have tried maniuplating the quartus makefile but no luck .I am abel to down load them independently ie my .elf or my hex file generated for my digital design but not both at the same time.If somebody could throw some light on this i would be greatefull even if they could comment on its feasability. Thanks and Regards, Rasquinha