Hi, is there a way to pay wages out of two separate accounts in the chart of accounts, i.e. wages - cogs and wages operations?

You cannot assign multiple expense accounts to a single wage pay type. Instead, create multiple pay types, assign each its own expense account, and then assign those pay types to the employee.

You can follow the steps in this article to create and assign pay types: Add or change pay types.
 

After that, update your Accounting Preferences in Payroll settings:

1. From the Home page, select the Settings (gear icon), then go to Payroll settings under YOUR COMPANY.
2. In Payroll Settings, scroll down and click Edit (pencil icon) for Accounting.
3. Next, select Wage expenses and click Edit (pencil icon).
4. Under 1. Where do you track employee wages in your QuickBooks chart of accounts?, choose Each employee's wages are posted to different types of accounts (ex: salary, contractor, and so on).
5. Assign the appropriate expense accounts to each wage type, then click Save.

Your payroll expenses will now be allocated to the correct accounts when you run future payrolls.

Let us know if you need anything else. We're here to help.