If you do not have ID fields already indicating how Salesforce Accounts and NetSuite Customers/Vendors are aligned, let's get things set up using the Breadwinner's Account Match process. If you do have ID fields and have performed a bulk match, you should still follow this procedure to ensure any exceptions are handled.
On the Breadwinner for NetSuite setup page, click the link "there are a few unmatched companies".
This will bring you to the Breadwinner Account Match for Companies page showing NetSuite Companies on the left and Breadwinner's educated guess as to corresponding Salesforce Account on the right.
To re-iterate the screen shot above, clicking the NEXT button will lock in your selections made above. Be sure to provide the correct selections, using suggested matches, looking up the correct account, or selecting Do Not Associate.
This process of tying NetSuite Companies to Salesforce Accounts is necessary to roll up corresponding NetSuite records to them correctly. Take your time and be diligent, it will be accomplished with a little bit of work.
Company Matching also has a Mass Update Option available.
Clicking the "Click here for a mass update option" will let you use filters to select and preview NetSuite Companies that meet specific criteria. You can then select to set "No Associated SF Account" which will indicate there is no associated connection and to ignore the NetSuite Company (customer/vendor). This selection does not prevent data associated with the NetSuite Company from being integrated to Salesforce, but does prevent the connection of that data rolling up to a salesforce account.