To better address your concerns, will Blizzard know that both accounts are you? Absolutely. Will you accounts both be actioned if one bots and one does not? That depends. You mentioned a Guild Bank. If both characters have access to that guild bank, their is potential that both accounts could be actioned. If your main benefits from the botting of the bot account WHATSOEVER, it will be guilty by association, and subject to the same actions as the bot account.
Hope that explains it.
TLDR Version: The only way to bot on one account and not bot on the other and remain safe is to make sure the non-bot account NEVER benefits from the actions of the botting account. Even then, Blizzard's TOS gives them the ability to ban, with or without reason, so it's anyone's guess when and now they'll exercise said power.