The base setup classes for flat tables are Mage_Core_Model_Resource_Setup and EAV entities Mage_Eav_Model_Entity_Setup.
Mage_Core_Model_Resource_Setup is used for non eav module and report and product alert admin modules table creation and it work on single table
Mage_Eav_Model_Entity_Setup is eav structural module. for customer ,product ,category module table creation and it work on multiple table
See at http://alanstorm.com/magento_advanced_orm_entity_attribute_value_part_1