You can sync payment fees as explained in the article. After that observe the payment fees as shown in this article.
(1)Now, go to your Xero Dashboard, click on “Reconcile Items” ( here I imported 4 transactions from bank)
(2) You will be redirected to “reconcile” screen in Xero. Before the reconciliation, ensure that “Balance in Xero” should be 0.
Now, identify the imported transactions from Shopify (here, my transactions are at bottom)
(3) Click on “Match” and again click on “Find & Match”
(4) It will list all the payments synced by Pipemonk, and go ahead by selecting the payments to the Number of L.H.S. matches with R.H.S. as shown. Here payments will be shown to reconcile if and only if your Deposit account is “Bank Account”.
After you see the amounts on LHS = RHS, click on “OK”
(5) Now after successful reconciliation, ensure that your Xero account shows the balance which is reconciled.
That's It. You have successfully completed the reconciliation process.