Hi there, @noemicastro.
Filing payroll forms from different software can be challenging. No worries, I'm here to assist you in handling situations like this.
While you have filed your W2s using Paychex, the threshold count will only based on the number of 1099s you prepare in QuickBooks Online. If it doesn't reach ten returns, you can manually file the 1099s you prepared in QuickBooks.
In case you need to make corrections to your 1099 forms after e-filing, refer to this article for guidance: Correct or change 1099s in QuickBooks.
Let us know if you have other questions besides filing threshold for 1099s prepared in QuickBooks Online. I'm always here to assist you.
