The Halacha states (Shulhan Aruch 456) states that Massa dough should be kneaded in small batches of less than the amount that requires taking Halla (approximately 3.5 lbs.). The Rabbis were concerned that if one would use a larger batch, it may be too big to handle at one time, and part of the dough would be left aside and become Hametz.
Nevertheless, it is still possible to fulfill the Misva of separating Halla from Massa. The individual small batches of dough can be connected so that, together, they reach the requisite measure necessary to take Halla. This method is often not practical because the Massa baking process is so rushed. The preferred solution is to first bake all of the Massot and then to gather them all in a single bin. Together, they form the requisite measure, and one Massa can be taken as Halla for all of the Massot.
It should be noted that on Yom Tob, it is prohibited to take Halla from Massot thqat were baked before Yom Tob. Therefore, all proper Hashgachot of Massot indicate that Halla has already been taken.
Taking Halla from Massot baked on Yom Tob presents a special challenge as to what to do with the separated dough. It cannot be given to a Kohen, since our dough is all Tameh (ritually impure). It cannot be burnt, as is usually done, since it is prohibited to burn holy items, which will not be eaten on Yom Tob. Letting the dough sit until after Yom Tob would allow the dough to become Hametz on Pesach. While theoretically, the dough could be immersed in very cold water to suspend the leavening, this is not recommended. Rather, Maran says that the best option is to take Halla after the Massot are already baked. That way, the Halla can be set aside until after Yom Tob and burned.
SUMMARY
Massa should be kneaded in small batches of under 3.5 lbs.
Halla should be taken from the Massa after it is already baked.
