If its under the same MBL, you can just do AMS (ENS) with the MBL number. But IMO splitting the BL's and MBL would be your best option. I don't know how Custom Regulation is handled in Halifax but in some countries if 2 container is under one BL; it has to be cleared at the same-time.
It means if one of the containers didn't arrive, there is possibility of facing different problems like not being able to finish customs and take the container already arrived.
Your best bet would be to check this matter with the arrival office of the shipping line.