Pace vs. Heart rate

So, this morning I finally managed to successfully export my first speed workout with my Garmin watch. I was surprised at how easy 6x400 felt and totally annoyed with all of the beeping my watch did telling me that my heart rate was too high. I've figured out my past tempo and long runs with the Mcmillian pace calculator, but that's not how this speed workout was programed. The Garmin workouts are calculated with heart rate zones. I can't tell you how hard it was to slow down enough to get my heart rate low enough to stop the beeping in zone 2. So, which is better, a speed workout done by pace or heart rate? I've only been running with a Garmin watch for 1 1/2 months, so I'm still a little new to this even after 3 years or running...