Dear Jason:

Sorry to take so long to answer your question.

One does not need to have a "poor brain" to be confused about this. I think most people are confused about the definitions of soul and spirit.

These two terms are complementary and not sharply differentiated. The Catechism explains:

367 Sometimes the soul is distinguished from the spirit: St. Paul for instance prays that God may sanctify his people "wholly", with "spirit and soul and body" kept sound and blameless at the Lord's coming.[1 Thess 5:23]

The Church teaches that this distinction does not introduce a duality into the soul.[Cf. Council of Constantinople IV (870): DS 657] "Spirit" signifies that from creation man is ordered to a supernatural end and that his soul can gratuitously be raised beyond all it deserves to communion with God.[Cf. Vatican Council I, Dei Filius: DS 3005; GS 22 § 5; Humani Generis: DS 389]

From Modern Catholic Dictionary by John A. Hardon, S.J. Doubleday & Co., Inc. Garden City, NY 1980

Soul. The spiritual immortal part in human beings that animates their body. Though a substance in itself, the soul is naturally ordained toward a body; separated it is an “incomplete substance. The soul has no parts, it is therefore simple, but it is not without accidents. The faculties are its proper accidents. Every experience adds to its accidental form. It is individually created for each person by God and infused into the body at the time of human insemination. It is moreover created in respect to the body it will inform, so that the substance of bodily features and of mental characteristics insofar as they depend on organic functions is safeguarded. As a simple and spiritual substance, the soul cannot die. Yet it is not the total human nature, since a human person is composed of body animated by the soul. In philosophy, animals and plants are also said to have souls, which operate as sensitive and vegetative principles of life. Unlike the human spirit, these souls are perishable. The rational soul contains all the powers of the two other souls and is the origin of the sensitive and vegetative functions in the human being.

Spirit. That which is positively immaterial. It is pure spirit if it has no dependence on matter either for its existence or for any of its activities. God is uncreated pure Spirit; the angels are created pure spirits.

The human soul is more properly called spiritual. Although it can exist independent of the body, it nevertheless in this life depends extrinsically on the body for its operations, and in the life to come retains a natural affinity for the body, with which after the resurrection it will be reunited for all eternity. (Etym. Latin spiritus breath, life, soul, mind, spirit, power.).

The Catholic Encyclopedia notes the following on the soul and spirit:

Soul: The soul may be defined as the ultimate internal principle by which we think, feel, and will, and by which our bodies are animated.....

Spirit: In Theology, the uses of the word are various. In the New Testament, it signifies sometimes the soul of man (generally its highest part, e.g., "the spirit is willing"), sometimes the supernatural action of God in man, sometimes the Holy Ghost ("the Spirit of Truth Whom the world cannot receive").

The use of this term to signify the supernatural life of grace is the explanation of St. Paul's language about the spiritual and the carnal man and his enumeration of the three elements, spirit, soul, and body. (1 Thessalonians 5:23, Ephesians 4:23).

We must be careful not to entertain the error that man is comprised of three elements (spirit, soul, and body). We are body and soul.

As St. Thomas Aquinas delineates, all life has soul:

Vegetative soul: Plants have this form of soul. It is the life force that animates all living things.

Sensitive soul: Animals have a vegetative soul that animates them and a sensitive soul that allows them to interact with their environment. This requires an awareness of the environment which plants do not have and an inclination to move toward or away from what is perceived. Thus, knowledge and appetite are the two functions characteristic of animals.

Rational soul: Human beings have all three forms of soul. The Rational soul is that which is created by God in His image. Neither plants nor animals are made in the image of God. This "image" includes the intellect that can understand eternal things (awareness of our own mortality and the life to come). It is the will that may conform itself to the will of God. It includes the creative and intellectual faculties of man.

The Rational soul can also be called the "spiritual soul" in that it includes not just the material soul (by which we think, feel, and will, and by which our bodies are animated) but also includes the immaterial and spiritual, the supernatural life of grace. It gives us the character of immortality. These things animals and plants do not have.

In the simplest terms, soul is that which animates us, allows us to feel and think. The spirit gives us the supernatural and spiritual faculty to receive God's grace. It imbues our soul  (that thinks, feels, and wills, and by which animates our bodies) with that which animals and plants do not have: the supernatural life of grace and immortality in the image of God.

I hope this is a little clearer than mud. 

God Bless,
Bro. Ignatius Mary