How did Nathanael see the angels of God ascending and descending on the Son of Man? In Jesus' encounter with Nathanael, Jesus concludes the conversation by indicating that Nathanael, as well as others, would see the angels of God ascending and descending on the Son of Man.  


  43 The next day Jesus decided to go to Galilee. He found Philip and
  said to him, “Follow me.” 44 Now Philip was from Bethsaida, the city
  of Andrew and Peter. 45 Philip found Nathanael and said to him, “We
  have found him of whom Moses in the Law and also the prophets wrote,
  Jesus of Nazareth, the son of Joseph.” 46 Nathanael said to him, “Can
  anything good come out of Nazareth?” Philip said to him, “Come and
  see.” 47 Jesus saw Nathanael coming toward him and said of him,
  “Behold, an Israelite indeed, in whom there is no deceit!” 48
  Nathanael said to him, “How do you know me?” Jesus answered him,
  “Before Philip called you, when you were under the fig tree, I saw
  you.” 49 Nathanael answered him, “Rabbi, you are the Son of God! You
  are the King of Israel!” 50 Jesus answered him, “Because I said to
  you, ‘I saw you under the fig tree,’ do you believe? You will see
  greater things than these.” 51 And he said to him, “Truly, truly, I say to you, you will see heaven opened, and the angels of God ascending and descending on the Son of Man.”  John 1:43-51 ESV


So, in what manner did Nathanael "see the angels of God ascending and descending on the son of Man?"
According to someone in this question (moved from christianity to hermeneutics):


  First, the phrase "the angels of God ascending and descending" links Jesus' statement back to Jacob's dream in Genesis 28. In that story Jacob himself glimpses a new reality. He says, "Surely the LORD is in this place, and I was not aware of it. How awesome is this place! This is none other than the house of God; this is the gate of heaven." In connecting himself to this, Jesus is perhaps indicating that what Jacob saw, Nathanael will soon see in the Son of Man: namely, the presence of the I AM, the "house of God" and the "gate of heaven" (cf. John 8:58, John 2:19-22, John 10:1-9).


Also according to bible.cc:


  Heaven open - This is a figurative expression, denoting "the conferring of favors." Psalm 78:23-24; "he opened the doors of heaven, and had rained down manna." It also denotes that God was about to work a miracle in attestation of a particular thing. See Matthew 3:16. In the language, here, there is an evident allusion to the ladder that Jacob saw in a dream, and to the angels ascending and descending on it, Genesis 28:12. It is not probable that Jesus referred to any particular instance in which Nathanael should literally see the heavens opened. The baptism of Jesus had taken place, and no other instance occurred in his life in which it is said that the "heavens were" opened.


As both quotations seem to say that it has something to do with Jacobs Ladder I think that it is safe to say the same. Also it is interesting to note that Nathanael was a descendant of Jacob. This link here also talks a little about this topic, saying:


  this passage shows Nathanael to be a thoughtful and reflective sort of person.  The statements of Jesus Christ about being an Israelite relate to his descent from Jacob, who was certainly a man full of guile and deceit during his early life.  That said, it would appear as if Nathanael was under the fig tree (a common representation of a philosophical sort of person) thinking about the dream of Jacob where angels went up and down the stairway to heaven, showing the relationship between heaven and earth and the possibility of communication between the two realms.  This musing on deep and spiritual matters allows Jesus Christ to call him as a member of the twelve without hesitation or complaint.


I don't know if people dislike so many quotations, but I found that they all relate quite well to the subject. I don't know. Think what you will from the quotations and links. What i get from it is that it was more of one of Jesus' encrypted sayings, not really meaning exactly what he says.