Peter, ask Marketo Support to set up a sync filter for you. It will look for a field that indicates whether a record should be synced or not. So you could indeed use a checkbox like "Sync to Marketo" and use that for the filter (check with Support, the reverse "Do Not Sync to Marketo" may also be possible). You can have only 1 field that indicates to sync or not, so most customers have a Workflow in SFDC to set that field automatically based on criteria.