There shouldn't be any problem syncing your SFDC instance to a new Marketo instance, as long as neither has been synced to SFDC/Marketo before. Marketo makes use of a User within SFDC to perform the actions necessary, so it will be like adding a new employee to your instance.
Marketo Support can set up a filter for your sync, but this works best with Leads and Contacts, and can cause problems if it's done with any other object. (Accounts, Opportunities, etc)
What we usually recommend is creating a custom boolean field on the Lead and Contact object called Sync To Marketo. Then we place a filter based on that field, and any Lead or Contact that has that field checked will sync over, while all others are ignored.
Let me know if you have any other questions.
It should also be possible to have the Marketo User only have access to that one Account/Contact/Lead. This isn't really ideal though.
Why do you want to do this in this way right now?
The other things to consider are any fields Pardot created in SFDC and whether or not those could sync to Marketo. You can block the Marketo User from seeing those too. I suggest working with a consultant or your CRM admin on a migration plan before you turn on the sync.