I will elaborate little if you still have the problem.
Quote:
All i see is just two tables after synchronization complete
As I understood you have many tables in Source and Target and after you 'Compare' Schemasync tree-view shows only two tables. This is because schema sync identified all other table's schema is same for both source and target.
If you like to see all tables including identical-schema tables, do the following:-
i) Select both source & target databases
ii) Un-check all the check-boxes in the right pane under section “Hide and Ignore Objects” (For you case you must un-check the option “Identical”)
iii) Click on 'Compare button.
Please see the screen-shot attached.