payment of gst

For Example: HDFC Bank A/c GST

For Over the Counter payment through authorised banks for deposits up to ten thousand rupees per challan per tax period.

For Both Cash and credit transactions you need to create the challan 

Dashboard>>Payment>> Create challan.>> payment method you can choose pay over the counter then it will show the list of Bank accounts

try with option,

so far we haven't paid in cheque but you can try the above option if you wish