Kain originally discovered the centre element of the Balance Emblem (which was likely the 'Balance Fragment ' and gifted him with the 'Balance Reaver') in The Chapel of the Sarafan Stronghold, upon returning to the Stronghold in Nosgoth's early history, a few years after the events of Soul Reaver 2 . Kain surmised that the emblem was of Ancient Vampire origin and that it's display in the Chapel indicated Moebius intended for him to find it. Moebius all but confirmed this when they met later on in the Stronghold.It enabled him to pass the 'Blessed Barriers ' and enhanced his charged and Reaver Spell attacks.
Kain would discover further Pillar orientated fragments of the Balance Emblem throughout the game:
Later on in the stronghold he discovered the Flame/Conflict Fragment, which granted him the Flame/Conflict Reaver and allowed him to perform Fire attacks and upgraded his Telekinesis accordingly, the Reaver Spell was much in the vein of Blood Omen's 'Inspire Hate ' spell.
The Lightning/Energy Fragment was found in the Vampire Citadel, In the Water Forge, which gave him the Lightning/Energy Reaver and gave an ability which appeared to be a modified Lightning ability from Blood Omen (seen used in a similar manner by the Hylden Lord in Blood Omen 2 and Kain himself in Legacy of Kain: Soul Reaver and Soul Reaver 2 )
The Time Fragment was also in the Vampire Citadel, in the Light Forge . This granted Kain the 'Time Reaver', which slowed the movements of Enemy characters, much the same as Slow Time artefacts from Blood Omen: Legacy of Kain .
As noted above, the Balance emblem's various upgrade fragments were based upon the various pillars (with Flame representing Conflict and Lightning representing energy), as such, it is likely they were a development of the Pillar Glyphs concept removed from Soul Reaver 2.
Though stated to be complete when Kain receives the Time Fragment, the Balance Emblem was originally supposed to have fragments for each of the pillars - the game is missing Mind, Nature, States and Death. It is currently unknown what the powers of these fragments would be, or if they will feature in future titles.