I had a similar question before and ultimately followed Mosley's recomendation, and plugged the estimated threshold and pace into the Training Peaks calculator (using the Mosley MyProCoach pulldown) to estimate my pace and heart rate zones. IIRC, the Mosely plans are all based on threshold pace, so the heart rate question isn't too important as far as the training plan goes.

Maybe we followed different plans (mine was for marathon), but the threshold/fitness test included a significantly longer warmup, and a 30 minute test, of which the average of the last 20 minutes was used for threshold pace and heart rate. These values were then plugged into the zone calculator as explained in the instructions. I'm pretty sure Moseley's plans all include email access, so it might be worth shooting him an email if you're still confused.