Just to add an obvious note: if a duplicate Lead is only in Marketo, you will have to merge it in Marketo (because at least 1 of the duplicate leads is not in SFDC).
Every once in a while when you are merging duplicates in Marketo, it fails for an unknown reason. When trying to merge the same records in SF it works.
There really is not a right answer, it's whatever you feel comfortable with.