I agree with the views submitted by the experts above. In addition to their views I would like to state as under:
Since capital goods of value upto ₹ 10,000/- is allowed to be treated as input and the entire cenvat credit on that is allowed to be taken in the same year, I would prefer to suggest that the entire invoice value should be booked in RG23C. And while utilising the credit entire credit should be debited to the account by mentioning the reference of said amendment.
And in Accounting package SAP, when Capital goods entry is passed usually, 50% of the credit is debited to 'Capital Cenvat Account' and balance 50% gets debited to 'Cenvat on Hold A/c'. And the credit of the amount lying in this account is taken credit in following year.
Now when the capital goods of value upto and above 10K is received under single invoice, then questions arises that how to account it in the books. I would suggest the querist to ask his IT help desk to create a separate tax code for the capital goods of value upto 10K, so that the entire credit on capital goods upto value of ₹ 10K is debited to 'Capital Cenvat Account' and for the capital goods of value above ₹ 10K is accounted as per existing practice as mentioned in the beginning of this para.
Hope the above suggestion is welcome. If not, request the learned experts to share their opinion on the same. Thanks.