Sacred Spots - Hindu worship sites before the popularity of temples

Ramanuja, a Vaishnava master from the fourteenth century researched the Pancharatra books related to worship traditions which had been handed down for millennia in the Indian subcontinent. He had taken up the study of the Pancharatra texts after having observed confusing worship practices in temples in Tamil Nadu. He later brought structure and much uniformity to worship practices based on his research.  The Pancharatra texts describe five distinct modes of invoking the unseen, the all pervading divinity into a recognizable structure.

The first mode is called "Sthandila" which is understood to be a small piece of land worthy of hosting the divine energy. The fire altar used in Vedic Yagnas was constructed in a carefully chosen spots of land or "Sthandila".  Ancient Yogis and Siddhas used their divination skills to choose worship spots where large temples structures arose eventually during historic centuries. A third of historic temples in South India are associated with a Rishi as the originator as they had chosen the spot. The fifty one Shakti Stalas found across India are considered as natural energy spots where mother energy had descended during an earlier era. There are temples in each of the Shakti Sthalas today.

A Yantra is often located beneath the main idol or Murthy in temples. A Yantra, such as the Sri Yantra, is a geometric design powers the idol in these temples. The Yantra, called as the "Mandala" forms the second mode of invoking the divinity according to Pancharatra texts. A water filled pitcher or a Kalasha with a coconut covering its mouth is common sight in many Hindu worship rituals. The annual rejuvenation ceremony, or the Brahmotsava, is a mandatory celebration in very Hindu temple. Vedic mantras are first chanted to infuse the waters in the pitcher with the energy of the divine. This water is then poured on top of the idol to energize the Murthy. "Kumbha" or the water pitcher is the third mode of invoking the divinity. "Archa" or the idol itself is only the fourth mode of invoking the divinity.
Shakthi Shalas in India

Pancharatra tradition originated during the time of Krishna, an Avatar or an incarnation of the divine. Historians have confirmed that texts related to temple worship were in wide circulation only by the sixth century CE. These texts contain chapters on the science of designing townships, homes and temples which alludes to the fact that the science of designing cities evolved around temple construction.  Historians such as Fergusson, Cunningham and Havell had suggested that the principles of Vastu Shastra or designing townships were developed in the ancient cities of the Harappan civilization between 6000 BCE and 3000 BCE.