Should the president or congress rule the country

No, and they don't, one does not rule over the other.
The president can not make a law, only sign ones passed. Pressident can veto laws, but congress can over rule him if a large enough group agrees.
Using a two or three party system, the idea is, that it is not easy to over rule president unless something is really the will of the people.
** well that is suppose to be how it works.

The Supreme Court is the one that worries me, since they often as of late, been "writing law" into their decissions, not merely ruling on the case before them Since they can strike down even the will of the people, they have more of the controlling power.

The people are sovereign. All branches of government exist to serve the people . They were never intended to rule . I think each branch should perform their designated roles as described in the Constitution.