The Nephites, understandably, had a difficult time understanding Isaiah. As Nephi points out, they didn’t know concerning the manner of prophesying among the Jews. This was intentional on Nephi’s part, for their works were works of darkness (v. 2). The Jews had a way of prophesying which could confuse just about anyone:
"The prophets sometimes speak of future events as present, because they are present to them in their visions. For instance, ’Unto us a Child is born.’ (Isa. 9:6)
"Similarly, they sometimes speak of the future as already past. For instance: ’He hath borne our grief and carried our sorrows; yet we did esteem him stricken, smitten of God, and afflicted.’ (Is. 53:4)
“Another peculiarity is that the prophets sometimes group together future events very much as one combines stars into constellations in the wide expanse, according to their apparent position to an observer on earth, rather than their actual distance from each other.” (Reynolds and Sjodahl, Commentary on the Book of Mormon, vol. 1, p. 370)
We have several advantages which help us understand Isaiah better than the Nephites did. Today, we have the entire Old Testament history to read. We have other prophets, like Jeremiah, Ezekiel, and Zecharaiah, which prophesied in a manner similar to Isaiah. We have linguists and scholars helping us understand the poetic forms of Hebrew writings. But more than all this, we have the advantage of other scriptures which teach us about the writings of Isaiah. There are interpretations of his writings in the New Testament, Book of Mormon, and Doctrine & Covenants. Lastly, we have the benefit of history on our side. All the things that Christ did during his mortal ministry are easy to understand when looking through the “retrospectoscope.” Nephi emphasizes this point later. He explains that when men see Isaiah’s prophecies being fulfilled they will finally understand their meaning, in the days that the prophecies of Isaiah shall be fulfilled men shall know of a surety, at the times when they shall come to pass (v. 7).