Sja has only one requirement: primary key must be defined for all tables that you want to sync. The speed of the sync is influenced by the structure of tables, but there is no sja specific recommendation as sja uses standard SQL commands to retrieve and manipulate data.
Therefore in case of InnoDB tables sja honors the foreign key restrictions (in fact, it is not sja, the InnoDB table handler does the job), but sja can be instructed to turn FK checks off while syncing. This is highly recommended as it is difficult to force sja to sync tables in a particular order.