In QuickBooks, please note that it is not possible to match two downloaded transactions into a single entry. But, you can efficiently exclude these transactions and manually clear the paycheque to reconcile your books without issues.
To exclude transactions, kindly follow these steps:
- Go to the Transactions section, then select Bank transactions.
- Click the For Review tab.
- Select the checkbox next to each transaction you wish to exclude.
- Hit Exclude.

After which, manually clear the paycheque in the Chart of accounts. Here's how:
1. Go to Transactions, then select Chart of accounts.
2. Find the account holding the split payment transactions, then choose Account history.

3. Select those payment transactions you want to clear.
4. Under the check column, mark C for these transactions.
5. Hit Save.
For further guidance on the reconciliation process, you might find this article helpful: Reconcile an account in QuickBooks Online.
If you have additional questions about managing transactions in QuickBooks, please feel free to leave a comment.