Hello there, raine.
QuickBooks Checking account isn't available in QuickBooks Desktop (QBDT). We can only use it through QuickBooks Online or QuickBooks Money. Thus, switching over to QBDT won't cause anything. However, you will need to consider the cost of QuickBooks Desktop itself.
In QBDT, you can set up for instant deposits. I recommend checking this article for more detailed steps and information: Deposit customer payments into your bank account in minutes. Additionally, you can read through this resource to get answers to frequently asked questions about QuickBooks Checking.
Still, I highly suggest contacting QuickBooks Payments Support. They can provide more details about handling your QuickBooks checking account after migrating to QBDT.
Have you previously used QBO and now prefer to switch to QBDT? I'm also providing these articles for more details on moving your books to QBDT.
You can visit again if you have more concerns about QuickBooks. I'll make sure to help you in any way that I can and provide details you need.
