You need a program called avrdude to upload the binary onto your target, and modify the parameters according to your setup and target:
mcu=atmega8
f_cpu=16000000
format=ihex
rate=19200
port=/dev/ttyusb0
programmer=stk500
target_file=test.hex
avrdude -F -p $mcu -P $port -c $programmer -b $rate -U flash:w:$target_file
If you're on a Debian or an Ubuntu machine, you should be able to do this to install avrdude:
sudo apt-get install avrdude
Otherwise you should be able to grab the sources from here and build it yourself.
Also there is a comprehensive Makefile that you could use to build and upload to your Arduino which again uses the similar avrdude commands to upload to the target. After changing the parameters in the Makefile, run make upload to upload the hex file to the target.
NOTE: You need to have gcc-avr and avr-libc packages installed to build the binaries (which from the question looks like you're already doing).
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