How a field collection item is linked to a node
If you check admin/structure/field-collections, you will find the machine name of you collections in the first column. Prepend the machine name with "field_data", just like any other field, and you will find a table with an "entity_id" column. 
In my case I have a collection called field_coworkers, and with

SELECT entity_type, entity_id FROM field_data_field_coworkers;


I can find the entities, that the fields are attached to.