These two names for God show different facets of God's power. El Shaddai is used a lot sorrounding God's promises, especially the promise of descendants to Abraham and Jacob. I would imagine that by the time Jacob heard the promise of nations he would have been a bit cynical, there had only been two sons born to his father and only two born to Abraham. Then God reveals Himself as the Almighty God. Almighty, able to fulfill the promise.
Almighty is also used a lot in Job, describing how God is Almighty when He provides and also Almighty when He takes away.
El Elyon is used talking about God's power and dominion and soveringty. Nebuchadnezzar spoke of the Most High when his senses returned to him and he finally understood God's rule over the heavens and the earth.
El Shaddai and El Elyon - God not only has the power to fulfill His promises, and the soveringty and dominion to see it done. The God who protects His people and destroys His enimies, who is just and righteous in His judgement. Who gives rest in His shadow.