It makes no difference.
Lets suppose you paid Rs. 90 as Advance Tax. The cess thereon @ 3% works out to Rs. 2.7. The total advance tax paid by you is Rs. 92.7.
Now the tax is Rs. 100. The cess thereon @ 3% works out to Rs. 3/-. The total tax payable by you is Rs. 103.
Now if you check calculations,Rs. 92.7 is also 90% of Rs. 103/-.
What you are perhaps trying to do is that Rs. 90 includes cess. The assessed tax is Rs103, in which case the advance tax payment will be less than 90% of assessed tax. However, this computation is not correct. You cannot compare oranges with apples.