Am I doing this on the side on which I removed the yellow stuff, or the side on which the HD rests normally?

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You're going to be applying heat to the ATI chip directly. If you're not too keen on disassembling the entire computer to remove the logic board, all you have to do is open the display and hang it off of the edge of your work surface and you can heat-gun away (too much heat will hurt the LCD). The hard drive doesn't care so much, so long as the heat gun's temperature isn't over about 800 degrees F. Any more than that, tho, and you're better off taking the logic board out completely to avoid damaging the other components.