please help its urgent

Hello experts

Please tell me the following query soon

We have received an intimation u/s 143(1) from bangalore for financial year 2007-08 requiring tax payable as it has not taken tds into account.we have drefted a reply letter for that already.

But now i want to ask this problem is being faced by many in the upcoming years also so to avoid the same what can be course of action for f/y 2008-09,2009-10 so that we dont have to face such kind of intimation again.can we do anything in advance like transferring file to delhi etc. or anything else.