New updation and rule gst

as you fill all the detail on gst portal , and go for make payment tab, it is automatically calculated IGST Credit against CGST first and then if IGST Credit remains it is setoff against SGST. 

But when i changed it manually the tab turned red doesnt that indicate  erroneous return? 

if it shows red, you have to check again, if you fill return online it is automatically setoff against your credit with tax liablity. 

suppose you have IGST credit rs. 40000, and your sgst and cgst tax liablity rs, 25000 each . first out of this 40000 setoff against cgst liability of rs. 25000 and balance will be setoff against sgst. and for  remaining balance of sgst you have to create challan. and paid the liability. after made a payment make setoff. and go to file a return.

i think from above example. it is clear for you.