If you're only worried about querying said checkboxes for a positive boolean (IE search for all that have flag checked), then just set up as you've described, and set the relation to allow for creation of records in the filemaker table via the relationship.
No need to create an entire matching set of records (and continously check for new records), but rather, the action of checking a box creates the related FM record.
Beware of the performance issues that can come from relating ESS directly into FM. The more records you get, the slower related tasks (IE finds) will perform.
As Mike said,
Your strategy will work. ESS does take some finesse with large record sets. The feature set is easy to use and get started with, but it can be very frustrating to make things work acceptably in practice. The trick is controlling the records in the SQL database that are accessible from Filemaker.
Let us know how you make out and where you get stuck.
Send a note to Filemaker and let them know you like and are using this feature along with the issues that are causing you problems. This feature set could be improved dramatically with a few updates, but that is most likely to happen with support from the Filemaker community.