That is the right paragraph. But I think that the language of Bonaventure is a bit confusing when translated into English. When he says that everything is in God, he's making a allusion Francis' Canticle of the Creature. We see God reflect in all things, because as St. John says in his Gospel, "all things came into being through him."
Your formation director has the right idea, but he or she is not using the language correctly. But the idea is correct. All things come into being through God and all things exist because God has called them into existence and he sustains all life. However, the danger to be avoided is to remember that God does not have control over all creation. He gives nature, man and angels free will. He does not interfere in those laws. Once he created free will and the laws that govern his creation, they exist without his interference, except in the cases of miracles. In those cases, when God does intervene it is for the good of the Church.
The pantheist believes that God is literally in everything that he has created. Therefore, God is found in a tree. If you root out the tree, you do violence to God. The panetheist believes that everything is literally in God. This means that we exist in God's mind. Therefore we are not independent from God. However, if we are not independent from God, that would mean that we do not have free choice. In which case, every sin is really God's fault, because we are in him and we do everything through his will. Every natural disaster is God's fault, not the laws of nature at work. Because nothing works independently God created everything, but keeps it all in his mind. In the end, we are only in God's mind. We are not a separate reality. This is wrong. If we existed in God's mind or within God, then there woiuld have been no need for Christ to become flesh. What for? God would have been able to save us by osmosis. Does this help?
Francis, thank you for sharing the wonderful story about your grandchild. I will say many prayers for her parents asking God to bless their courage and their fidelity to him. I'm sure that you're very proud of them. I understand that genetic counselors mean well, but they do not understand that this is not a package of genetic material. It's a person with the same rights as everyone else. As I tell our parents to be, "We have laws that protect the rights of people with disabilities, why shouldn't this protection cover their rights from the moment of conception?" Aborting a disabled child protects the pocketbook of the state, not the person with disabilities. Before I became a religious, I was married. My wife died many years ago. But we had three children. One died with her in an auto accident. I raised the other two. My son has autism. We were told to terminate the abortion. Today, he is a junior in college and lives with his older sister. He is very independent, thanks to many years of therapy, medication, special schools, tutors, and a lot of love and patience on my part and that of the family on both sides: my wife and mine. When I made final vows in March, he was one of the two witnesses that canon law requires. It was wonderful to have my son stand beside me as I consecrated my life to follow Christ in the sandals of St. Francis. I will keep you and your holy family in my prayers, please pray for me.