For thoughtful people, how they pray for the soul is governed by how they believe God acts. So, for example, if they believe God changes people's souls so that they make new and right choices, then they will ask God to make those soul-changes through evangelism and nurture. But not everybody is thoughtful about the way they pray. They don't think about what view of God is behind their praying.
So what I suggest is that we learn first to pray for the soul from the way the Bible prays for the soul. If we do that, then our prayers will probably be good prayers, and in the process we will also learn about how God acts. Here is the way I pray for my soul. I use these prayers over and over again-for myself and my children and wife and for the staff and the elders and for all the church. This is the meat and potatoes of my prayer life.
The first thing my soul needs is an inclination to God and his word. Without that, nothing else will happen of any value in my life. I must want to know God and read his word and draw near to him. Where does that "want to" come from? It comes from God. So Psalm 119:36 teaches us to pray, "Incline my heart to Your testimonies and not to gain."
Next I need to have the eyes of my heart opened, so that when my inclination leads me to the word I see what is really there and not just my own ideas Who opens the eyes of the heart? God does. So Psalm 119:18 teaches us to pray, "Open my eyes, that I may behold wonderful things from Your law."
Then I need for my heart to be enlightened with these "wonders." I need to perceive glory in them and not just interesting facts. Who enlightens the heart? God does. So Ephesians 1:18 teaches us to pray "That the eyes of your heart may be enlightened."
Then I am concerned that my heart is fragmented and that parts of it might remain in the dark while other parts are enlightened. So I long for my heart to be united for God. Where does that wholeness and unity come from? From God. So Psalm 86:11 teaches us to pray, "O Lord, I will walk in Your truth; unite my heart to fear Your name."
What I really want from all this engagement with the Word of God and the work of his Spirit in answer to my prayers is that my heart will be satisfied with God and not with the world. Where does that satisfaction come from? It comes from God. So Psalm 90:14 teaches us to pray, "O satisfy us in the morning with Your lovingkindness, that we may sing for joy and be glad all our days."
But I don't just want to be happy in my own little private world with God. I want my happiness to be as full as possible for spreading and expanding for others. I want to be strong in joy. This will make me durable in the face of threats or adversity. Where does that strength and durability come from? It comes from God. So Ephesians 3:16 teaches us to pray, "That God would grant you, according to the riches of His glory, to be strengthened with power through His Spirit in the inner man."