Our marketo instance is integrated with SFDC (call it as 'SF1') . We are migrating data from a different salesforce instance (Call it as 'SF2') to SF1. We are de-dupling data in SF1 and SF2. However there can be some common accounts and Contacts which have same email id, data in both SF1 and SF2. So will this create duplicate data in our marketo instance as it's been integrated with SF1 salesforce instance? If yes how to avoid it. If it's not possible, can we separate both the records in marketo instance so that we can easily identify from which salesforce org the data is from?
Yes, if you create a new record in SF1, it will sync as a new record (or dupe) to Marketo. Marketo does not dedupe from SFDC originated records.
You could add a flag in SF1 to say "From SF2=TRUE" and this may help. I'd get demand tools or ringlead to clean this up from both sides.