What happens if a manual order is placed in my brokerage account that is AutoTrading?

Such orders are called "external" since C2 did not send them. If you place a manual order in your account from the broker's software, web site or over the phone, AutoSync will be disabled and an automated email will be sent to you to inform you of this.

Why do we disable AutoSync? Because we don't know exactly what you are trying to do, or even which system your manual order belongs to, and if left enabled, AutoSync would reverse your order.

When you re-enable AutoSync from the C2 AutoTrade Control Panel, the AutoTrade server will resynchronize your brokerage account with your strategies according to your AutoTrade permissions.

Suggestion: Open a brokerage account dedicated just to AutoTrading and keep your manual trading in a separate account. Most brokers have a simple process of creating a sub-account that allows you to do this without any additional cost.