This lesson from the Workbook contains pointers on two different levels. This is not fostering "level confusion", but taking the approach of offering advice for differing levels of understanding in students. To offer what cannot be understood is a sign of poor teaching. Thus, the Workbook, being a self-study guide, often gives teachings on multiple levels, like a holographic instruction. Gurdjieff's idea of a legominism is of similar import.
"I am affected only by my thoughts." (Lesson 338)
On a surface level, we are familiar with the effects of thoughts on our state, behaviour and relative state of consciousness. The Course makes the point repeatedly that modifying behavious is secondary to modifying thought and belief, which in turn affect behaviour. The "I" referred to here, is that of the changeable, personal self- the ego. The self we made and have identified with up until finding out the truth.
"It needs but this to let salvation come to all the world. For in this single thought is everyone released at last from fear. Now has he learned that no one frightens him, and nothing can endanger him. He has no enemies, and he is safe from all external things. His thoughts can frighten him, but since these thoughts belong to him alone, he has the power to change them and exchange each fear thought for a happy thought of love. He crucified himself. Yet God has planned that His beloved Son will be redeemed."
A preliminary step is offered here. The insight that the world is not cause, but rather an effect, brought about by habitual thought. In seeing the world as effect, it may be exchanged for the "happy dream" wherein guilt, victims, and separation may be released. Fear thoughts may be recognised and purposely exchanged with thoughts of love. This is the thinking behind much of the "New Thought" movement, and most positive thinking teachings. Many religions make use of substituting fear thoughts for loving thoughts. It certainly works as an aid in exchanging a fearful world for one that is happier to live in. Recall, "My thoughts are images that I have made".
However, this isn't the end, but rather just the first step. Many spiritual systems do end here, incomplete due to still being trapped in a happier dream, but a dream of separation nonetheless. The ego does not end. Duality still persists no matter how "happy" we attempt to make the world. The perceiver still sees the world.
"Your plan is sure, my Father,—only Yours. All other plans will fail. And I will have thoughts that will frighten me, until I learn that You have given me the only Thought that leads me to salvation. Mine alone will fail, and lead me nowhere. But the Thought You gave me promises to lead me home, because it holds Your promise to Your Son." (Lesson 338)
There can only be one will ultimately in all creation- that of the Source. Setting up the ego as a separate 'will', thus results in having to deal with fearful thoughts UNTIL the separation is healed and no more. How? By finding one's true Identity, the Self, which is referred to here as the Thought (of God). This is not a thought in the usual sense of the word, but THE "Thought of God" (ie pure consciousness) that exists prior to, and part of, all seeming arising and passing thoughts.
This primal "Thought", when sought with earnestness, leads to salvation, and the undoing of the separation, which is not done of myself (as "I"), but by the Holy Spirit, as God's promise that His Son (the Self) may come to know Itself once again. The Lesson thus achieves its aim, starting in time, and ending back in eternity.