I've paid and employee in 2 transactions and now when reviewing the bank transactions it doesn't automatically match to the payroll postings, how do i match them?

Are you trying to match the payroll journals to the employee payments? Do the amounts match? If you click on the payment in banking and go to find a match are they there?

Yes that’s what I usually do to match them. The issue is I’ve paid them in 2 transactions, for example total payment should have been £500 and I’ve paid £200 and £300 so it doesn’t let me allocate them unless I resolve the reconciling difference and I don’t know where to put the difference if that makes sense? Looking at it now I think I should have put it as an advance payment before running payroll so I will remember that for next time!

Thanks for adding some details of your concern, info1403.

Unfortunately, we're unable to match the two payments to a single transaction since their amounts aren't the same. Please take note that we can only match transactions with the same amounts in QuickBooks Online.

To ensure that your payroll records are accurate, you'll have to exclude those two downloaded transactions on the Banking page. Once done, you'll have to manually clear them in the register so you can easily reconcile the transactions. I'll show you how:
 

1. Select Accounting from the sidebar menu.
2. Go to Chart of Accounts.
3. Find the account holding the transaction, then click View register from the Action column.
4. Locate the payments, then review the check column.
5. Select the transaction and then keep clicking the box from the Check column the box until it shows C. This process will mark the transaction as cleared.
6. Click the Save button to save the changes, then close the account register.

I also encourage reading these articles to help manage your downloaded bank transactions in QuickBooks Online:
 

• Categorize and match online bank transactions
• Setup bank rules to speed up the review process

I'm just a few clicks away if you have any other concerns or questions about bank transactions and reconciliation. I'll always have your back.