Hasan,
Can you please advise me about the best practices to bring in the New company to the Exisitng R12 ledger. Acquired company Ledger is on Legacy System. Scenario: 4C's are same, One BG, New company will have its' own LE.

Sorry this is a very open ended question. A White paper could be written on it. If you have a specific question, I can answer it for you. Not sure from which perspective you are looking for best practices but here are few points:
1) Verify if the new company could use the same ledger options (Retained Earnings account, Reversal Set, Period Management, Suspense Account etc).
2) You have to see the impact on existing components e.g. FSG Reports, Mass Allocations, Recurring Journals etc and see if these components have to be modified.
3) Opening balances have to be migrated from legacy system. You can bring them using a manual journal (ADI option is there).
4) Impact has to be analysed in subledgers e.g. check formats, payment profiles etc.
5) Impact has to be analysed on custom components (interface programs etc).