I separate after the dough is made, put it in a glass bowl, and the on the microwave. I cook it for a minute or so and turn it over to cook it for another minute. Sometimes a third minute is needed. Never just stick it in foir several minutes without checking it and flipping it. I have had dough balls catch on fire like that. Mamash flames and smoke.
For amount to require Hafrasha, I try to take off according to Chacham Ovadia, which I believe is according to the Rambam in the 2nd Mishnah in Edyuot, which is 1660 grams – about 3.5 pounds.