You get to the point where the bowing just comes naturally, without much thought. I actually find myself doing little "head-bob" bows for a few days after returning home from Japan - along with occasionally popping out with "sumimasen" or "ohayo gozaimasu." I get strange looks from my collegues until I re-acclimate.
Of course, I occasionally get strange looks from them anyway. The old mileage runner habits, you know.
JR