Hi Megan,

Let me guide you how to stop generating auto journal entry number for your payroll account. Here's how:

1. Click on the Settings icon in QuickBooks Online.
2. Click on Account & Settings.
3. Click on Advanced tab.
4. Under Other preferences turn off Warn me if duplicate journal number is used. 
5. Click on Save and Done.

Send us a reply here if you need more help with your payroll file.