Which cells were five Amos tall?
Rashi: All of them were. Their total height was 15, plus the thickness of the ceilings.
Why does it say "Al Kol ha'Bayis"?
Radak: This is like Im Kol ha'Bayis. Also "va'Yavo ha'Anashim Al ha'Nashim"(Shemos 35:22) and similar verses. The cells were not on the Bayis, rather, around it.
Perhaps this means after he finished the entire Bayis (including the roof), he built the cells, like Malbim explains (but he does not learn this from "Al" - PF).
What is the meaning of "va'Ye'echoz Es ha'Bayis"?
Rashi: This is the upper roof [of the Heichal]. The Sefun mentioned in verse 9 was the roof of the Aliyah.
Radak #1: The cell 'held' the Bayis with cedar beams, which were near the wall of the Bayis. 'Va'Ye'echoz' refers to the roof; the verb is Po'el Yotzei Shelishi (Shlomo (a) 'held' the Bayis (b) with the beams (c)).
Radak #2: 'Va'Ye'echoz' refers to the cell; it 'held' the Bayis.
Gra: He connected the roofs of the cells to the Bayis via cedar wood.
Malbim: He rested the ceiling of the cell on the Migra'os (recessions) of the walls of the Bayis, like it says above (verse 6) "l'Vilti Achoz b'Kiros ha'Bayis."