I have made a bebot module to keep track of my tokens. You can try it out if you want.
When ingame send this: /tell Isendyourcmd !tokens add shards 100 - would add 100 Atlantean Shards.
For more info: /tell Isendyourcmd !help tokens
Its all based on manual input by the player for each character.
Other open modules check: Helpfull modules for bebot, available to all ingame