How do I arrange my sefirot in book shelves? Is there any order to be considered? What other things to look for? Thank you

Shalom, Thank you for your question. You asked about “sefirot” but I assume you mean “sefarim” or holy books. There are laws about resting things on top of a Torah – including books of lesser holiness. However, on bookshelves, where the books are standing up straight, on next to the other, there is no problem of one being “on top” of the other. So, according to the halacha, there is no issue of how you might want to organize your Jewish bookshelf. On a practical level, you could organize them according to topic – Chumash, Tanach, Mishna and Talmud, Jewish thought, Prayer etc. May you merit to learn from your seforim, and grow in Torah.