Pricing exclusive of taxes in Sales Quote, Trial Balance adjustments

Hi,

I made few modifications in the ERP, I edited sales quotation, altered the unit price as exclusive of taxes and then added the taxes in the at the sub total. This alteration disturbed the tax calculation at the backed, then I edited the tax calculation formula in tax_calc.php file, Now it calculates the tax correctly but the other features and modules of the ERP are still assuming that my prices are inclusive of tax and due to this I am facing issues in GL accounts (i.e Sales Revenue, Sales, Receivables & etc).

Now here i think that I should not have edited the sales quotation in this way.
Is there any other way to create sales quotation mentioning unit prices exclusive of tax?
Or anyone can guide me to edit entire calculations in the GL.

Thanks