God created heavens and earth according to his own will and also determines his authority to rule over it, Matthew records in Matthew 20:15 Lord says Is it not lawful for me to do what I will with mine own? Is thine eye evil, because I am good? So the last shall be first, and the first last: for many be called, but few chosen.
Through holy sprit Paul speaks in Romans 9:20 O man, who art thou that repliest against God? Shall the thing formed say to him that formed it, Why hast thou made me thus? It is not worthy to question our creator as he already got right to have authority over us but to submit us to him ref. Eph 1:11 In whom also we have obtained an inheritance, being predestinated according to the purpose of him who worketh all things after the counsel of his own will.
Scripture defines that God has authority over all his creation (living, nonliving, material & Immaterial) there are many scripture references of Gods authority some are quoted here 1 Chronicles 29:11, Psalm 115:3, Isaiah 45:9, Ezekiel 18:4, Dan 4:34, Matthew 20:15, Rom 9:14-21; 11-36, Ephesians 1:11, 1 Timothy 6:15, Rev 4:11.
God not only created the universe but also preserves his works, considering example of machines the creator/maker or machine defines and performs maintainable and durable fix time to time to keep machine running, almost every one knows there is no self existing or self reviewing force exists but there is some external force that is required to perform the action and God is the external force that work to preserve and retain his works we read in Nehemiah 9:6 Thou, even thou, art Lord alone; thou hast made heaven, the heaven of heavens, with all their host, the earth, and all things that are therein, the seas, and all that is therein, and thou preservest them all; and the host of heaven worshippeth thee. And Col 1:17 stated he is before all things, and by him all things consist, some of the references are quoted here- Hebrews 1:3, Psalm 36:6, 37:28, 104:29, 66:9, Acts 17:28, Proverbs 2:8, John 10:28.
Concerning method of creation, although God creates all things according to his will and have authority over all his works he had given natural power to men (his images) ref. 1 Cor 12:6 and Acts 17:28 For in him we live, and move, and have our being; as certain also of your own poets have said, For we are also his offspring Men’s acts are evil that misuse or use natural power in evil ways.