intimaiton u/s 143(1)

I has filled my E-return for mar 2008 though intermediary on 2/6/2008. the intermediary has wrongly remitted my retrun thereafter the return was manually submitted on 19/6/2008 by the intermediary and acknowledgment given to me.

Now the IT is refering the innitial return and raising a demand for tax payment u/s 143(1) which need to be paid in 30 days. Please help ne how should i go about filling an application with AO u/s 154. Should i write a free form letter to the AO enclosing the copy of acknowledge return on 19/6/2008