Steps to follow:
System->GST Updates->Update Product Tax/HSN Using Purchase:-> Please run this option to correct tax types as per tax types entered in purchase invoices. Please give date range from 1st July to current date. This option will automatically change tax type in product & batch master as per the tax types entered in purchase invoices.
System->GST Updates->Update Tax Code in Retail Transaction:-> Please run this option to correct tax types in sales invoices as per tax types defined in Product/Batch master. This option will correct tax types in all invoices raised after 1st July under GST. Please select “Sales” in “Applicable For” and tick YES to “Replace By Tax Type Specified in Product Master”. Now select all Series, Master Group, Group, Attribute, Category & Product to update all transactions.
One more issue is that in Cross, you have provided discount in footer, which is calculated after tax and Tax is charged on amount before discount. Since all sales is inclusive of taxes, so customer is paying proper amount in any case. Please run following step to shift existing discount to product detail, so that tax is calculated after discount.
Sales->Daily Posting in Account:-> Please select date range from 1 July to current date and tick on “Shift Footer Discount to Detail Discount” option to repost discount given in invoice footer part to product wise detail discount. At present discount is after tax, it will shift to before Tax. When you give discount in sales invoice, please use Ctrl-B to give discount in product detail before tax.
Discount can be predefined for sales invoice in series, patient, doctor and product master. You can predefine discounts in these four ways and you can also enter/change discount in each product while billing. You can use Ctrl-B key to enter discount in all items of invoice or revise bill amount to discounted bill amount. Please do not use footer discount now. By entering discount using Ctrl-B, you will get same functionality and GST will be calculated after discount.