Well, there are quite a few ways they limited the power of the presidency.
1) They gave Congress the power to override the presidency.
2) Congress also had the power to impeach.
3) Congress can deny presidential appointments.
4) Congress ratifies treaties.
5) Congress controls the declaration of war.
6) Congress also controls the budget.
7) The judicial branch (Court system) can rule presidential actions unconstitutional.
8) Judges appointed by the President sit for life - no getting rid of them if they make a decision the President doesn't like!
Hope this helps!