Once your accounts have been produced if there is corporation tax to pay this will show in Ember as a liability of the business. This can be viewed in the 'money business owes' report.
If you have paid the tax this will no longer be a liability so it is key to record this to ensure you have an accurate view of what the business actually owes!
When categorising you must ensure the 'corporation tax owed' category is selected as shown below so that the payment nets off against the outstanding balance:
For more information on categorising a bank transaction, please see our article here
If you still can't categorise the transaction on your invoice after trying the above, please reach out to support.