HI Neelima,
Please check the below posts which talks about Migration -
For PO -
You will have to configure Interfaces for Proxy and IDoc based on Single stack methodlogy.
EDI - You will have to check feasibility of using B2B addon
I think it will not matter if you do in cycles or you do at once.
Also check below thread for reference.
Hope this helps -
Thanks
Ninad Sane