QB Issue Resolution:

It matters if your bank processes one ACH for the paydate, or will create individual entries in your account, seen on the statement. Bookkeeping matches reality.

I set up a Schedule for those employees paid by DD. You don’t use handwritten checks. You still go through the Payroll process. Segregate the DD people from the Printing Paycheck people.

If your bank uses an ACH template ending with one total from your checking account, then in QB, create a new bank account and name it Payroll Clearing. Run the DD payroll and “pay from” this account. Now, this account has the details and is running negative. Post a Deposit TO this account, and FROM checking. This Payroll Clearing account ends with a balance of 0, every time, if you did this correctly. Reconcile it to 0.

If your ACH process is going to be one paycheck at a time, but electronically, seen in your statement as individual entries, then this still is Paychecks, paid from Checking, but you can use Assign Check #. I put in DD1 and QB increments from there.

Resolution for Issue 'Direct Deposit through my bank, not QuickBooks.' available: Yes (Solved).
Source: Intuit Community forum.

Direct Deposit through my bank, not QuickBooks.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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