There are two settings for notifications:
1 - App global, used by default for all accounts: Menu -> Settings -> Message notificaitons.
2 - Per-account overrides. By default, none, but you can change them: long press the account -> Special settings -> message notifications -> enable the override and set to your preference.
I should note that Android doesn't "juggle" different LED colors coming from multiple notifications. It just uses the most recent color, it seems.
There is a third party app, called LightFlow, that can do this "color juggling", and it works with Aqua.