Upon character creation, each player starts with his chosen alignment (chaos, balance or order) on 100% .
During gameplay certain actions will trigger loss or gain of alignment with the factions. These values are taken into account immediately during certain interactions with those deities (purchasing temporary buffs etc), but the faction alignment will only get into effect upon the conclusion of an era.
The process at the conclusion of an era is described in the above referenced link to Campaign era.
At the end of that calculation (based on the 'snapshots' during each death) a player will have his faction changed or remain the same but his alignment percentages will change accordingly for the purposes of next era calculations.
The player won't be able to directly affect the outcome of this faction change.
Character has each faction alignement tracked as a total number gained in the era, total overall across all eras and current balance of each. He/she can spend the balance but it won't affect the total for an era or overall.
These numbers are tracked family wide.
Players will be able to change alignment only to the faction determined by their actions at the end of an era or by switching to another family of different alignment on another server.