Bhagavan Krishna in the Gita Chapter 15, Sloka 1 has remarked about a tree having its roots or origin above and branches underneath. This type of a tree is not noticed. This tree may be impermanent but its origin is indestructible. This tree is the corporeal frame. The Inherent-Intrinsic beyond the gross human frame, in other words the One Who has kept this body alive is Prana or Atma. This Prana or Atma is Imperishable. The body has originated from Him.
The root signifies the principal or the origin i.e. the Still state of Prana or Atma (the Infinite Soul). He prevails in the upper region i.e. between the Kutastha and the Sahasrara. He is Static. Dynamism originating from Him flows down the lower portion of the body that is attaning vibration manifests as the 49 airs like Prana, Apana, Vyana, Udana, Samana, Naga, Kurma, Krikara, Devdatta, Dhananjaya etc. thereby maintaining the body, thus the branches are beneath.
Kriyayoga is Brahmasadhana or else through the medium of this sadhana the purpose is to gradually overcome the kinetism of the lower portion, and eventually arrive at the upper portion of the body- the head or the region between Kutastha and Sahasrara cakra or at the state of stillness.
The technique of this sadhana mentioned in the Gita is represented as a symbol in the logo of the Mission's (Societies catering to the exclusive spiritual upliftment of humankind) therefore the logo is the symbol of Brahmasadhana which shortly will become the imperative practice of humankind ushering the influence of Satyayuga after the world fully undergoes a cataclysm.
The arrow indicates releasing the obstruction of the Anahata Cakra. This is an imperative exercise of any Kriyaban prior to the attainment of the state of moksha or salvation. Since this is an extremely vital process in the path of Kriyayoga, the practisant yogi or Kriyaban has to surrender to the Lotus Feet of the Sadguru without which moksha is impossible. "Aage marzi Maalik ki" as Lahiree Mahasaya stated.