Joins between tables work slightly different in OQL.
If there is an association between two enities, you can do an OQL join on them without an ON clause.
Assuming both FeeSchedule and FeeAgreement are in the CFT module, to get the ID of all FeeSchedules that are associated to a FeeAgreement
SELECT FS.ID, FA.ID FROM CFT.FeeSchedule AS FS INNER JOIN FS/CFT.FeeSchedule_FeeAgreement/CFT.FeeAgreement AS FA WHERE FS.Status = '_Final'
Also note here that the association is written out completely, including module names and including the 'right' side entity.
Have a look at the OQL documentation to find out more..
Finally, a good help to validate your OQL is to compose it using a DataSet, it will show you whether your OQL is valid, just like with xpath.
Hope that helps!