Placing Sefarim on top of each other:
It is permitted to place a Chumash on top of Nevim or Kesuvim. However one may not place a Nevim or Kesuvim on top of a Chumash, and one may not place a Chumash on top of a Sefer Torah. One may place a Kesuvim over a Navi. It is permitted to bind a set of Tanach in one binding in any order that one chooses. [There is no order regarding Sefarim of Torah Shebal Peh such as Gemara, Mishneh and their commentaries, and they may thus be placed on top of each other. Some however are stringent in this regard. However, they may not be placed on top of a Chumash, Nevim or Kesuvim.]
The status of a Siddur:
A Siddur has the same status of holiness as a Sefer. Furthermore, the custom is to treat a Siddur with the same status as Nevim and Kesuvim. One may not however place a Siddur on top of a Chumash. If the Siddur contains Tehillim at its end [as is common by the Tehilas Hashem Siddurim], then it is questionable as to its status, and practically, one should treat it as Nevi’im, although is not to place it on top of Tanach.
The status of a Tanya:
The Chabad custom is to treat a Tanya with the same respect as a Chumash and hence we do not place other Sefarim over it, including a Chumash. One may not however place a Tanya on top of a Chumash.
Placing Tefillin over or under Sefarim, and other items:
Coming up in future Halacha.
 Michaber Y.D. 282:19; See Hiskashrus 709; Ginzei Hakodesh 3
 Michaber ibid
 Rama ibid
 Rama ibid; Ran Megillah 8b; Tosafus Baba Basra 13b “Rebbe Yehuda”
 Based on Rama ibid regarding Nevim and Kesuvim and the fact that there is no such law mentioned regarding the Sefarim of the oral Torah. So is also understood from M”A 25:4. See Ginzeiy Kodesh 3:29
 Leket Yosher Yoreh Deah p. 59 that his teacher, the Terumos Hadeshen would not place the Sefarim on top of each other; It is told that the Rebbe once removed a Sicha from on top of a Shulchan Aruch. [Yoman 28th Sivan 1967]; See Ginzei Kodesh ibid
 Riy Migash 92
 See Soles Belula 25:9; Or Tzadikim p. 10; Beis Haroeh p. 2; Machzik Bracha 25:12; Kaf Hachaim 25:101
 Hiskashrus ibid; Ginzei Hakodesh ibid; See Aliba Dehilchasa 24 p. 29 in name of Rav Chaim Kanievsky and Rav Elyashiv that a Siddur has the status of Torah Shebal Peh, like a Gemara and in name of other Rabbanim that it has the status of Torah Shebichsav;
The reason: This is due to the great amount of verses from Tanach quoted there, as well as due to the fact that it contains the name of G-d.
 Rav SZ”A in Mivakshei Torah 4:19, 235:3
 See Rivivos Efarim 1:119 for various opinions and in conclusion that the Siddur is to be placed on the Tehillim; However, see Shevet Hakehasi 2:299 that it has the status of a Gemara even if it has Tehillim at its end
 See letter of Rebbe Rayatz brought in Kitzurim Veharos on Tanya p. 118; Maaseh Melech p. 7
 Pashut. And so is told that the Rebbe at times went out of his way to remove a Tanya from on top of a Chumash.