The wisdom behind reading the Shajrah for the mureed in a specific silsila, is that he remains in touch with this chain or channel which has been formed by Allah (Almighty and Glorious is He) for him. When we read the shajrah we establish our connection with the Holy Prophet Muhammad (Peace be upon him, his family and companions) through that chain. This is a special channel to obtain special favors of Allah (Almighty and Glorious is He). As the angels are appointed functionaries to perform specific tasks the Aulia are functionaries to assist man on the spiritual quest. The recitation of the shajrah is to stay in touch with the link of the spiritual chain and the spiritual masters who make up the spiritual chain. The link is kept fresh and "rust free"; by virtue of the mureeds daily recitation of the Shajrah. By reciting the Shajrah, one repeatedly renews one's pledge with the Masters of the Order; and this contact brings great results in this world and in the hereafter.
Allah (Almighty and Glorious is He) says in Holy Qur'aan the 17th Sura, Bani Israel verse 71:
"One day we shall call together all human beings with their respective Imams/Leaders".
The explanation of this verse is that each follower will be asked to be behind his leader/guide that he followed in this world. This verse is indicative of the fact that the mureed will be called upon on the Day of Qiyaamah to be behind his Shaykh, and under the flag of the spiritual order that he belongs to.
It is of utmost importance that the mureed recites the Shajrah with understanding, sincerity and feeling. This will stir his soul; which is invaluable in the spiritual progress of the mureed. The attention of the Shuyukh (plural of "Shaykh") is also drawn to the person and they respond spiritually, with great affinity - both in this life and after death.
The Shajrah expresses certain feelings with the specific intention of "Wasila" present; but at the same time, it should be kept in mind that everything invariably is from the blessing of Allah (Almighty and Glorious is He).
The Shajrah is usually recited after Salaatul Fajr or after Salaatul Esha. The time for reading should be kept constant. The wazaaif prescribed by the Shaykh to a mureed should be consistently recited, for this serves as a "polish" for the heart