Just to be clear, you have to move more than the CPU in order to do a proper transplant. The CPU/NAND/Baseband and EEPROM, along with the TouchID sensor need to be moved over to a host board if you want to retain your data.
As for the CPU, you can try to move the two layers at once or move them separately. If you apply too much heat, you will not have a choice but to separate them.
I will say this, perhaps more for the benefit of others who will find this Q&A in the future, transplanting a CPU (successfully) is extremely difficult and very few people can do this reliably as of this writing. Even if everything goes well, this is a low probability repair. If you are not incredibly experienced, you will fail doing this. Quite honestly, it's probably easier to fix your damaged board than to do a transplant.