What are the Shekufim?
Rashi: They are like a Mashkof (lintel) on which the door knocks.
Radak: They are windows. They are called so for one is Shokef (looks through) them - "va'Yashkef Avimelech Be'ad ha'Chalon" (Bereishis 26:8). Malbim - on both sides to the length and width there were cut stones, and windows for air.
Where were the Shekufim?
Rashi: The 15 planks did not cover the entire 100 Amos length of the house. To cover [the remainder], he made small planks on small beams from one row of Kerusos Arazim 1 to another. There are Shekufim on each side. The small planks are on the Shekufim. The length of the small beams is along the width of the big beams that were put first.
Rashi (2): These are beams on top of the pillars; they joined one pillar to the next.
What is the meaning of "Sheloshah Turim"?
Gra: It is as if it says li'Sheloshah Turim; the three spaces below had windows.
Malbim: There were three windows one on top of another. There were three sets along the length of the house, on each side.
What is "u'Mechezeh El Mechezeh"?
Rashi: The ends of the planks of one Shekof are opposite those of another. Mechezeh refers to the end - "El Mechuz Cheftzam" (Tehilim 107:30). In the Mishnah, Chazis refers to the end, and in Tamid (29a), and in Bava Basra (2a) - he makes a Chazis from the outside. Yonason translates 'corner opposite corner.' However, he translated "Shekufim Atumim" (6:4) and "Revu'im Shakef" (verse 5) as poles.
Radak, Gra: Window opposite window. Malbim - i.e. windows on one side of the length were opposite those on the other side.