In Part I, you learned that the subjunctive mood is used whenever the speaker feels uncertain about the action of the sentence, or when the speaker is expressing a subjective opinion. In Part II, you learned the basic rules for conjugating regular verbs and stem-changing verbs. In this lesson you will learn how to conjugate verbs in the present subjunctive that change orthographically. That's a hard one to answer. There's another question, one that pertains to learning Spanish, that's much easier to answer.
Spanish spelling is nearly perfect phonetically.
That is, if you can pronounce it, you can spell it, and if you see it written, you can pronounce it. The answer is that the pronunciation came first. Later, an alphabet was developed to represent that pronunciation on paper. Fortunately, when the rules for the alphabet were developed, they were kept simple and straightforward. That is why, in Spanish, you can spell any word that you can pronounce, and you can pronounce any word that you see written.