Hello Sanjay
Not sure how to maintain alternate hierarchy. Need to check. But the hierarchy in MDG is standard. One more point when you use idoc based replication, system deletes entire hierarchy in ECC first and then replace it with MDG hierarchy. There is no delta update. Make sure you have back up of your hierarchy in ECC.
You can also download the hierarchy in MDG from ECC. See my document - how to load the finance master data in MDG.
Kiran