CENVAT credit can be availed by recording either a journal or debit note transaction in Tally.ERP 9 release 5.x onwards. In case of debit note the stock value is reduced to the extent of CENVAT credit availed and affect the cost of the stock items accordingly.
However, in case of journal voucher there is no implication on the stock summary. It is supported with a view to allow availing CENVAT credit without recording a debit note and without reducing stock value.
Both these methods can be used to avail CENVAT credit depending on your requirement. It is suggested to use debit note in case you want to update stock value to the extent of CENVAT credit.