1)
Why does it say "all that He desired, He did in Shamayim and Eretz"?
1.
Radak: This is unlike angels. They do no without Hashem's desire. All the Heavenly and earthly legions do not stop Him from doing His desire in Shamayim and on the land.
2.
Malbim: He created the entire creation as He wanted. Not only did He make Shamayim and Eretz - also in them, He does as He desires - light, clouds, luminaries, inanimate, vegetative, living, speakers (people) and fish in the seas and depths.
2)
What are "Yamim v'Chol Tehomos"?