This is a common misconception that various payment processors face.
While some payment processors act as ‘Digital Wallets’ wherein all the funds transferred to a user’s account sit in that account unless the user explicitly initiates a bank transfer. When the user is paying funds out, the money sitting in their account is used to make fulfill the payment request. ‘Digital Wallets’ hold their users’ funds and charge them when the money is transferred to a connected bank account.
Checkbook is NOT a ‘Digital Wallet’. We pride ourselves in not hoarding our users’ funds and charging them hidden fees during bank transfers. Checkbook facilitates payments by directly taking funds from the sender's bank account and depositing it directly in the recipient’s bank account.
During no part of this process are your funds stored with Checkbook. It is a simple pick up and drop transaction that is completed because of the infrastructure Checkbook has created.
Therefore, the short answer is, NO, Checkbook does not hold your money.