How do I merge the checking account that payroll is connected to with the checking account that was already set up for that same checking account?

Hello there, @info811.

You can merge two accounts into one as long as they are of the same level and have no sub-accounts. 

In the meantime, if you're merging bank accounts that have reconciliation reports, these will be deleted from the account that has been merged.

However, the reconcile status (R) will remain on the merge transactions. I encourage saving reconciled reports before merging your accounts.

To merge two accounts:

1. Click the Gear icon.
2. Choose Charts of Accounts.
3. Select Edit from the drop-down from the Action column.
4. Take note of the Name and Detail Type, and check if the Is sub-account option is marked. 
5. Hit Cancel to return to the Chart of Accounts.
6. Choose the account which you don't want to use, then click Edit from the drop-down in the Action column.
7. Make changes in the Name and Detail Type field. Mark Is subaccount as appropriate.
8. Hit Save, then select Yes to confirm.

For more detailed steps, you can check out this article:  How to merge accounts, customers, and vendors.

Also, I've attached this article to help you change the type of an existing parent account or sub-account in case you're merging account with sub-accounts:  How to change the type of an existing parent account or sub-account.

Drop me a comment below if you have any other questions about QuickBooks. I'll be happy to help you out.