Tax paid not applied when computing tax demand

I saw a Demand for AY 2008-09 from IT dept u/s 154.  I agreed to the Demand and made the payment.  After that I realize that in July 2008 I made a payment towards AY 2008-09 - but wrongly under the code for "Regular Assessment".  And in the corresponding return I did not mention the challan number details.  I guess that is the reason the paid amount did not get counted.

Now that I have realized my mistake and have payment challan details, etc. How do I approach the IT dept to have the paid amount counted?  I think it can be counted towards the interest on tax demand  (u/s 220(2) which I still have to pay.

If I should contact my AO for the same, what is the protocol?  Can I just send an email describing my problem?

Thanks