Firstly there is no amount payable u/r 6(3A). The amount payable is u/r 6(3) only. For the purpose of quantification though we need to revert to rule 6(3A).
To explain let me illustrate:
Rs. 1,000 is the total available credit paid by the assessee towards common input services. The previous year's ratio of Exempted goods and services to total goods and services (both exempted and taxable) comes to 60%, than out of Rs. 1,000/-, Rs. 600 (i.e. 60%) is amount quantified u/r 6(3A). The assessee shall avail Rs. 1,000 under Rule 6(1). Out of this it shall utilise Rs. 600 towards payments u/ r 6(3). Balance Rs. 400/- it could utilise for payment of duty on taxable goods or taxable services.
This is clear from congoent reading of
a) Rule 6(3) which is notwithstanding rule 6(1) and (2) and clearly provides for the what amount is payable, with
b) Explanation II, which talks about how the payment is to be made i.e. "by debiting the CENVAT credit or otherwise" with
c) Form ER-1, which at clause 8 point no. 13 clearly provides for disclosure of utilisation of CENVAT credits for payments of amount under Rule 6.
Thus in case if the whole amount of CENVAT for common input or input services are not to be utilised but only the amount proportiante to the amount used for taxable goods/ services, than one may directly resort to rule 6(2) and not come to rule 6(3) atall. It is only when the entire amount is to be utilised that the amount to be reversed is to be worked out u/r 6(3A).