I doubt we can do that through existing item master ... As per GST if i Sell item "A" within intra-state then I have to levy SGST @ 14% AND CGST @ 14% and When I sell the same Item "A" outside my state of registration then I have to levy IGST @ 28%. At present there is no linkage of item taxes with the customer account.
My suggestion to handle this .... in the HSN master you can add 6 columns
SGST, CGST,IGST for sales within state and SGST, CGST,IGST for sales outside state... wherein the users can define the tax rates applicable for both type of sales.
Then at the Sales invoice level system can identify the applicable taxes through HSN (HSN is linked with Item) and Customer GSTIN (if the first 2 Numbers of the customer GSTIN matches with my GSTIN then it is intra-state sales and if they do not match then it is inter-state sales).