Logos has a different option for Direct Deposit Payroll from those used in Ministry Connection that you may be able to take advantage of once Ministry Connection is stopped, depending on your Bank.
If your Bank works with Direct Deposit Nacha files, you may set up Logos Payroll for Direct Deposit ACH Processing.
If this is not an option for you, once Ministry Connection is turned off, you will need to go back to printing payroll checks. At that time, each employee record must be updated by removing the check-mark in the EFT Deposit field of the Salary Information Tab. (Note: If you are going to transition to the Nacha option, leave all employee records as they are and see the linked Help Article above.)
Once this has been completed, make sure you Reset All employees in the Payroll Process. You may go into Process Payroll, click Next, and click Reset All at your convenience. Then, just close out of Payroll until you are ready for the next Payroll Process.