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I would always use Marketo to import unless you had (and know how to use) Demand Tools for SFDC.
Once in Marketo, you can sort dupes by Name or Email to merge any that had different emails. I wouldn't worry about Company names.
Of course, when you import in Marketo, NEW records will go to SFDC as Leads.
Like Josh mentioned the big difference is the ability to create leads vs. contacts (cannot create in Marketo, but can in SFDC). Additionally, with a Marketo upload you can create a static list that keeps the records tied together without needing a field or campaign in SFDC.
If the companies already exist in SFDC and your list is pretty clean as it relates to the company names, I would upload in SFDC as it will automatically match them to the company. It would be great if you had a tool like Demand Tools or my favorite dupe tool, RingLead, to automatically remove dupes.
Whether you load in Marketo or SFDC, you can manipulate the data quickly and easily in Marketo (merging records, deleting outdated records, updating certain fields, etc.)
Hope that helps!