I cleared a check in old accounts in Excel then migrated to accounts manager.io software, now this cheque is deposited in bank after one month and bank clears it accordingly, How do I clear manager.io because it was booked and cleared in the excel account.
Welcome to the forum @Shafqat_Talkies,
In order to clear a Receipt or a Payment, you need to setup your Bank and Cash Account to accept pending transactions:
You should check the box that says 
Can have pending transactions.
See the following guide for more detail.
Then inside the Edit screen of your Receipt / Payment, you can set the cleared status. See this guide.
I have already been paid the cheque in excel accounts and then I transferred the current payable to manager.io, so the payment is now showing in the bank statement, now how do I clarify this payment in the bank reconciliation
Bank reconciliation is exactly what it says it is. See Reconcile bank accounts | Manager extracted but read all:
Bank reconciliation is the process of verifying your records of transactions posted to bank accounts against records of the institutions. (The term bank is used generically to refer to any institution from which you receive or can obtain statements, whether by mail or electronically.) To avoid potential problems caused by undiscovered errors, you should reconcile your bank accounts regularly.