OK - I'm not the best person to answer this (my first upload from a computer to a microcontroller was exactly yesterday, after much poring over the in-program help). BTW, if you haven't yet, you should read the AVR Studio online help; it's pretty nice actually. But in any case:
You save the file to that hold_servo.hex file as described before.
Start up AVR Studio.
Open file, and pick the hex file that you saved. I think at this point you see the program and it's english translation in the disassembler.
Plug your two servos into the ground/power/control pin triplets for PD0 and PD1 as described in the tutorial.
Plug the programmer into the computer's USB port and the other end onto the 3x2 header you made on your board
Plug the batteries into your robot.
Connect to the robot from AVR studio by pushing the button (and it's also in one of the menus at the top) shown here: http://www.societyofrobots.com/images/sbs_connect_AVR.png
And then there should be another button to actually program the microcontroller from there (I can check when I get home tonight), but it should be pretty obvious.
Write to Flash.
When it's done you unplug the batteries, then unplug the the programmer. Then you plug the batteries back into the board and your servos snap to zero.