I have multiple counties that I need to withhold taxes for employees. The 1st co set up has the type "IN - Counties" but the rest are user undefined. Any advice?

Welcome to the Community, @userjkardelisiu. I'd be happy to help with setting up local taxes.

QuickBooks Online Payroll (QBOP) calculates local taxes based on your IRS filing address. Your address determines the local tax jurisdiction: the city, county, and regional agencies where you'll owe payroll taxes.

To set up local taxes, here's how:

1. In the left menu, click Payroll.
2. Go to the Employees tab.
3. Locate and click the employee's name.
4. Under the Employee details, click the pencil icon beside Pay.
5. On the question about employee's withholding, select edit (pencil) icon.
6. Go to Local Taxes and mark the local tax jurisdiction.
7. Tap Done.

Once the local tax setup is complete, the system will calculate the local taxes for you. 

For more information on how to set up local taxes for the employee and company, see this article: Local tax setup and support: Main hub.

Here's also a great resource on how payroll works in QuickBooks Online including filing tax forms: Payroll 101.

If you have questions about payroll or any other QuickBooks topic, please don't hesitate to let me know. Have a great day.